Alignments for a candidate for asnB in Bradyrhizobium sp. BTAi1

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Bradyrhizobium sp. BTAi1

Align Putative asparagine synthetase [glutamine-hydrolyzing]; EC 6.3.5.4 (characterized)
to candidate WP_012045542.1 BBTA_RS26290 asparagine synthase (glutamine-hydrolyzing)

Query= SwissProt::P64248
         (652 letters)



>NCBI__GCF_000015165.1:WP_012045542.1
          Length = 656

 Score =  298 bits (763), Expect = 5e-85
 Identities = 231/670 (34%), Positives = 319/670 (47%), Gaps = 60/670 (8%)

Query: 1   MCGLLAFVAAPAGAAGPEGAD---AASAIARASHLMRHRGPDESGTWHAVDGASGGVVFG 57
           MCG+       AG   P GAD    A  + R +  + HRGPD SG+W  V G  G +  G
Sbjct: 1   MCGI-------AGLFRPGGADDSALAGIVGRMTAALAHRGPDASGSW--VSGRQG-IALG 50

Query: 58  FNRLSIIDIAHSH-QPLRWGPPEAPDRYVLVFNGEIYNYLELRDELRTQHGAV-FATDGD 115
             RL+I+D++ +  QP+      A  RY + FNGEIYN+L+LR EL     A  +    D
Sbjct: 51  QRRLAILDLSEAGAQPMH----SACGRYTITFNGEIYNHLDLRAELEDAAAAPNWRGHSD 106

Query: 116 GEAILAGYHHWG-TEVLQRLRGMFAFALWDTVTRELFCARDPFGIKPLFIATGAGGTAVA 174
            E +LA    WG    LQRL GMFAFALWD  TR+L  ARD FG KPLF           
Sbjct: 107 TETLLAAIRQWGLVPALQRLIGMFAFALWDAETRQLILARDRFGEKPLFYGWSGADLVFG 166

Query: 175 SEKKCLLDLVELVGFDTEIDHRALQHYTVLQYVPEPETLHRGVRRLESGCFARIRADQ-- 232
           SE K L       G+   +D  AL  +    YVP P T+ R VR+L    F    AD   
Sbjct: 167 SELKAL---AAHPGWAPSLDRAALTDFMRYSYVPAPATIWRDVRKLPPASFVAFVADAGP 223

Query: 233 -LAPVITRYFVPRFAASPITNDNDQARYDEITAV---LEDSVAKHMRADVTVGAFLSGGI 288
             +P    Y+  R        D      + I  +   L  +V +   +DV +GAFLSGG+
Sbjct: 224 GTSPTAQSYWSLRDTVVAAQGDRISGESEAIARLEQLLSTAVKRQCLSDVPLGAFLSGGV 283

Query: 289 DSTAIAALAIRHNPRLI-TFTTGFEREGFSEIDVAVASAEAIGARHIAKVVSADEFVAAL 347
           DS+ I AL      + + TF+ GF   G++E + A   A+ +G  H    V A   +  +
Sbjct: 284 DSSTIVALMQAQASQPVRTFSIGFAEGGYNEAEDARKVAQHLGTDHTELYVDARTAMEVV 343

Query: 348 PEIVWYLDEPVADPALVPLFFVAREARKHVKVVLSGEGADELFGGYT--IYREPLSLRPF 405
           P++    DEP AD + +P   VA+ AR+HV V LSG+  DELFGGY   ++   L  R  
Sbjct: 344 PKLPRIYDEPFADSSQIPTHLVAQLARRHVTVALSGDAGDELFGGYNRHVWGSALQAR-L 402

Query: 406 DYLPKPLRRSMGKVSKPL-PEGMRGKSLLHRGSLTLEERYYGNARSFSGAQLREVLPGFR 464
             +P PLRR++G     + PE     +LL+     L  R          A+L  ++    
Sbjct: 403 GRVPMPLRRAIGAALGAIAPEP--ADTLLNMLQPVLPARLRVRHAGDQVAKLARIVAADG 460

Query: 465 PDWTHT-------DVTAPVYA--ESAGWDP------------VARMQHIDLFTWLRGDIL 503
            D  +        D  A V A  E A W              + RM   D  ++L  DIL
Sbjct: 461 FDGLYRTLCSIDQDPRATVVAGEERASWAASEMKQLRGQISLLDRMTLADSLSYLSDDIL 520

Query: 504 VKADKITMANSLELRVPFLDPEVFAVASRLPAGAKITRTTTKYALRRALEPIVPAHVLHR 563
            K D+  MA +LE RVPFLD +V   ++R+PA  K+     K+ +R+ L   VPA ++ R
Sbjct: 521 QKVDRAAMAVALETRVPFLDRDVVEFSTRVPASMKVRDGRGKWLVRQVLYRHVPADMIDR 580

Query: 564 PKLGFPVPIRHWLRAGELLEWAYATVGSSQAGH--LVDIAAVYRMLDEHRCGSSDHSRRL 621
           PK GF +P+  WLR G L  WA   +  ++     L     V RM +EH     +H+  L
Sbjct: 581 PKTGFSIPLDAWLR-GPLKSWAGDLLSPARLKRQGLFAPTRVTRMFEEHLSRRHNHAYWL 639

Query: 622 WTMLIFMLWH 631
           W +L+   W+
Sbjct: 640 WNVLMAEAWY 649


Lambda     K      H
   0.323    0.138    0.428 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 1104
Number of extensions: 68
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 652
Length of database: 656
Length adjustment: 38
Effective length of query: 614
Effective length of database: 618
Effective search space:   379452
Effective search space used:   379452
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 54 (25.4 bits)

Align candidate WP_012045542.1 BBTA_RS26290 (asparagine synthase (glutamine-hydrolyzing))
to HMM TIGR01536 (asnB: asparagine synthase (glutamine-hydrolyzing) (EC 6.3.5.4))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.aa/TIGR01536.hmm
# target sequence database:        /tmp/gapView.2431485.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01536  [M=517]
Accession:   TIGR01536
Description: asn_synth_AEB: asparagine synthase (glutamine-hydrolyzing)
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                             Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   9.9e-143  462.7   0.0   1.2e-142  462.4   0.0    1.1  1  NCBI__GCF_000015165.1:WP_012045542.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000015165.1:WP_012045542.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  462.4   0.0  1.2e-142  1.2e-142       1     517 []       2     585 ..       2     585 .. 0.87

  Alignments for each domain:
  == domain 1  score: 462.4 bits;  conditional E-value: 1.2e-142
                             TIGR01536   1 Cgiagivdlkakake.eeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlseg.aQPlsnek.e 70 
                                           Cgiag++    + ++     + +m+ +lahRGPDa+g w +  +++ +lg+rRLai dlse+ aQP++++  +
  NCBI__GCF_000015165.1:WP_012045542.1   2 CGIAGLFRPGGADDSaLAGIVGRMTAALAHRGPDASGSWVS-GRQGIALGQRRLAILDLSEAgAQPMHSACgR 73 
                                           ********9988888766899********************.899***************999*******9** PP

                             TIGR01536  71 vvivfnGEIYNheeLreeleekGy..eFetksDtEViLaayeewg.eelverLeGmFAfalwdekkgelflaR 140
                                           ++i+fnGEIYNh +Lr+ele++    +++++sDtE +Laa+++wg   +++rL GmFAfalwd+++++l+laR
  NCBI__GCF_000015165.1:WP_012045542.1  74 YTITFNGEIYNHLDLRAELEDAAAapNWRGHSDTETLLAAIRQWGlVPALQRLIGMFAFALWDAETRQLILAR 146
                                           *******************98654338********************************************** PP

                             TIGR01536 141 DrlGikPLYyaseqgkllfaSEiKallalkeikaeldkealaelltlqlvptektlfkevkelepakal.... 209
                                           Dr+G kPL+y+  +  l+f+SE+Kal a++  +++ld++al++++ +++vp + t++++v++l+pa+ +    
  NCBI__GCF_000015165.1:WP_012045542.1 147 DRFGEKPLFYGWSGADLVFGSELKALAAHPGWAPSLDRAALTDFMRYSYVPAPATIWRDVRKLPPASFVafva 219
                                           ******************************99**********************************9998999 PP

                             TIGR01536 210 ....dgeekleeywevekee......vkeseeelveelrelledavkkrlvadvpvgvllSGGlDSslvaaia 272
                                                 + + ++yw+++++       + + e+e++++l++ll  avk++  +dvp+g++lSGG+DSs+++a++
  NCBI__GCF_000015165.1:WP_012045542.1 220 dagpGTSPTAQSYWSLRDTVvaaqgdRISGESEAIARLEQLLSTAVKRQCLSDVPLGAFLSGGVDSSTIVALM 292
                                           886533444555****9998777776555578999************************************** PP

                             TIGR01536 273 kkeaksevktFsigfedskdldeskaarkvadelgtehkevliseeevlkeleevilaleeptairasiplyl 345
                                           +++a ++v+tFsigf+ +  ++e++ arkva++lgt+h+e+++++ ++++ ++++ ++ +ep+a++++ip+ l
  NCBI__GCF_000015165.1:WP_012045542.1 293 QAQASQPVRTFSIGFA-EGGYNEAEDARKVAQHLGTDHTELYVDARTAMEVVPKLPRIYDEPFADSSQIPTHL 364
                                           ****************.9******************************************************* PP

                             TIGR01536 346 lsklarekgvkVvLsGeGaDElfgGYeyfreakaeeale.................................. 384
                                           +++lar++ v+V+LsG+ +DElfgGY+++    a +a                                    
  NCBI__GCF_000015165.1:WP_012045542.1 365 VAQLARRH-VTVALSGDAGDELFGGYNRHVWGSALQARLgrvpmplrraigaalgaiapepadtllnmlqpvl 436
                                           ********.******************9987544443335799998888888888888877777666666654 PP

                             TIGR01536 385 .....lpeaselaekkl....................llqaklakeselkellkakleeelkekeelkkelke 432
                                                +                               l    +++ ++  +  +a++ ++ ++ +  ++e+k+
  NCBI__GCF_000015165.1:WP_012045542.1 437 parlrV----------RhagdqvaklarivaadgfdgL----YRTLCSIDQDPRATVVAGEERASWAASEMKQ 495
                                           433330..........0333444555566666644433....3344444444444444444444444433333 PP

                             TIGR01536 433 e....seleellrldlelllsdllrak.DrvsmahslEvRvPflDkelvelalsippelklrdgkeKvlLrea 500
                                                s l++++ +d   +lsd+++ k Dr++ma  lE RvPflD+++ve+  ++p+++k+rdg+ K+l r++
  NCBI__GCF_000015165.1:WP_012045542.1 496 LrgqiSLLDRMTLADSLSYLSDDILQKvDRAAMAVALETRVPFLDRDVVEFSTRVPASMKVRDGRGKWLVRQV 568
                                           34556******************************************************************** PP

                             TIGR01536 501 aeellPeeileRkKeaf 517
                                           + +++P ++ +R+K +f
  NCBI__GCF_000015165.1:WP_012045542.1 569 LYRHVPADMIDRPKTGF 585
                                           ***************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (656 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 21.98
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for Amino acid biosynthesis