Alignments for a candidate for asnB in Azohydromonas australica DSM 1124

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Azohydromonas australica DSM 1124

Align Putative asparagine synthetase [glutamine-hydrolyzing]; EC 6.3.5.4 (characterized)
to candidate WP_029000198.1 H537_RS0126035 amidotransferase 1, exosortase A system-associated

Query= SwissProt::P64248
         (652 letters)



>NCBI__GCF_000430725.1:WP_029000198.1
          Length = 647

 Score =  319 bits (817), Expect = 3e-91
 Identities = 232/647 (35%), Positives = 324/647 (50%), Gaps = 46/647 (7%)

Query: 1   MCGLLAFVAAPAGAAGPEGADAASAIARASHLMRHRGPDESGTWHAVDGASGGVVFGFNR 60
           MCG+        GA   E A     + R +    HRGPD  G  H       GV  G  R
Sbjct: 1   MCGITGLFDT-RGARNFERA----TLQRMNEAQHHRGPD-GGDLHL----EPGVGLGHRR 50

Query: 61  LSIIDIAHSHQPLRWGPPEAPDRYVLVFNGEIYNYLELRDELRTQHGAVFATDGDGEAIL 120
           LSIID+A   QPL           V+VFNGEIYNY EL  EL+   G VF T  D E I+
Sbjct: 51  LSIIDLATGQQPLF----NEDGSVVIVFNGEIYNYQELVPELQAL-GHVFRTHSDTEVIV 105

Query: 121 AGYHHWGTEVLQRLRGMFAFALWDTVTRELFCARDPFGIKPLFIATGAGGTAV-ASEKKC 179
             +  WG+  +QRLRGMFAFALWD   +  F ARD  G+KP+  A    GT V  SE K 
Sbjct: 106 HAWESWGSACVQRLRGMFAFALWDRNQQTFFMARDRLGVKPMHYALLDDGTLVFGSELKT 165

Query: 180 LLDLVELVGFDTEIDHRALQHYTVLQYVPEPETLHRGVRRLESGCFARIRADQLAPVITR 239
           LL      G   +ID  A++ Y  L YV EP  + R  R+L +G    +R  Q      +
Sbjct: 166 LL---AHGGLRRDIDPLAVEEYFALGYVAEPRCIFRQARKLPAGHMLLLRRGQPLAEPQQ 222

Query: 240 YFVPRFAASPITNDNDQARYDEITAVLEDSVAKHMRADVTVGAFLSGGIDSTAIAA-LAI 298
           Y+  RF         D     E+ A + +SV   M ADV +GAFLSGG+DS+A+ + +A 
Sbjct: 223 YWDLRFTLDRKIGLQDACA--ELDARVHESVRLRMIADVPLGAFLSGGVDSSAVVSHMAE 280

Query: 299 RHNPRLITFTTGFEREGFSEIDVAVASAEAIGARHIAKVVSADEFVAALPEIVWYLDEPV 358
                + T +  F    F+E + A   A+     H   +V +D+F   +  +    DEP 
Sbjct: 281 LSQGPVNTCSMAFADPAFNEAEFARMVADRYRTNHFVDMVDSDDF-GLVDTLAAMYDEPY 339

Query: 359 ADPALVPLFFVAREARKHVKVVLSGEGADELFGGYTIYR-EPLSLRPFDYLPKPLRRSM- 416
           AD + VP + V + AR HVKV LSG+G DE FGGY  YR   +  R    LP  LRR + 
Sbjct: 340 ADSSAVPTYRVCQLARTHVKVALSGDGGDEAFGGYRRYRMHMMEERMRSALPLALRRPLF 399

Query: 417 GKVSKPLPEG------MRGKSLLHRGSLTLEERYYGNA---------RSFSGAQLREVLP 461
           G + +  P+       +R K+     S T  + Y+ +          R F+GA  RE+  
Sbjct: 400 GTLGRLYPKADWAPQVLRAKTTFEGMSRTAAQAYFHSMARLRQPLRDRLFTGALKREL-- 457

Query: 462 GFRPDWTHTDVTAPVYAESAGWDPVARMQHIDLFTWLRGDILVKADKITMANSLELRVPF 521
                ++  +V       +   DP+A +Q+IDL TWL  DI  K D+ +M + LE+R P 
Sbjct: 458 ---GGYSALEVFERHARRAGTDDPLALVQYIDLKTWLIDDINAKVDRASMEHGLEVREPL 514

Query: 522 LDPEVFAVASRLPAGAKITRTTTKYALRRALEPIVPAHVLHRPKLGFPVPIRHWLRAGEL 581
           +D E+   A+ LP+  K++    K+  ++ALEP +P  VL+RPK+GF VP+  W R    
Sbjct: 515 MDHELVEWAATLPSSLKVSAGEGKHVFKKALEPRLPHDVLYRPKMGFSVPLARWFRGPLR 574

Query: 582 LEWAYATVGSSQAG-HLVDIAAVYRMLDEHRCGSSDHSRRLWTMLIF 627
                + +G + A     D+  + R++D+H  G+ DHS  LWT+L+F
Sbjct: 575 QRLRESLLGGAMADTGWFDVRLMGRLVDQHESGAHDHSTALWTLLMF 621


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: 1109
Number of extensions: 66
Number of successful extensions: 9
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: 647
Length adjustment: 38
Effective length of query: 614
Effective length of database: 609
Effective search space:   373926
Effective search space used:   373926
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_029000198.1 H537_RS0126035 (amidotransferase 1, exosortase A system-associated)
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.1882437.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   9.5e-149  482.6   0.0   1.1e-148  482.4   0.0    1.0  1  NCBI__GCF_000430725.1:WP_029000198.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000430725.1:WP_029000198.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  482.4   0.0  1.1e-148  1.1e-148       1     517 []       2     561 ..       2     561 .. 0.90

  Alignments for each domain:
  == domain 1  score: 482.4 bits;  conditional E-value: 1.1e-148
                             TIGR01536   1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlsegaQPlsnek.evv 72 
                                           Cgi+g++d + + + e++++++m+e+++hRGPD+  ++ +    +++lghrRL+iidl +g+QPl ne+ +vv
  NCBI__GCF_000430725.1:WP_029000198.1   2 CGITGLFDTRGARNFERATLQRMNEAQHHRGPDGGDLHLE---PGVGLGHRRLSIIDLATGQQPLFNEDgSVV 71 
                                           *********9987779********************9988...7***************************** PP

                             TIGR01536  73 ivfnGEIYNheeLreeleekGyeFetksDtEViLaayeewgeelverLeGmFAfalwdekkgelflaRDrlGi 145
                                           ivfnGEIYN++eL  el++ G+ F+t+sDtEVi++a+e+wg ++v+rL+GmFAfalwd++++++f+aRDrlG+
  NCBI__GCF_000430725.1:WP_029000198.1  72 IVFNGEIYNYQELVPELQALGHVFRTHSDTEVIVHAWESWGSACVQRLRGMFAFALWDRNQQTFFMARDRLGV 144
                                           ************************************************************************* PP

                             TIGR01536 146 kPLYyase.qgkllfaSEiKallalkeikaeldkealaelltlqlvptektlfkevkelepakal.....dge 212
                                           kP++ya   +g+l+f+SE+K lla+   ++ +d  a+ e+++l +v++++++f++ ++l++++ l     ++ 
  NCBI__GCF_000430725.1:WP_029000198.1 145 KPMHYALLdDGTLVFGSELKTLLAHGGLRRDIDPLAVEEYFALGYVAEPRCIFRQARKLPAGHMLllrrgQPL 217
                                           *****98779*******************************************************9*988888 PP

                             TIGR01536 213 ekleeywevekee.vkeseeelveelrelledavkkrlvadvpvgvllSGGlDSslvaaiakkeaksevktFs 284
                                           ++ ++yw+++ +  +k  ++++++el+  ++++v+ r++advp+g++lSGG+DSs+v++ +++ ++++v+t s
  NCBI__GCF_000430725.1:WP_029000198.1 218 AEPQQYWDLRFTLdRKIGLQDACAELDARVHESVRLRMIADVPLGAFLSGGVDSSAVVSHMAELSQGPVNTCS 290
                                           88888*****99878889******************************************************* PP

                             TIGR01536 285 igfedskdldeskaarkvadelgtehkevliseeevlkeleevilaleeptairasiplyllsklarekgvkV 357
                                           ++f+ +++++e+++ar vad  +t+h   +++++++   ++ +  + +ep a+++++p+y +++lar + vkV
  NCBI__GCF_000430725.1:WP_029000198.1 291 MAFA-DPAFNEAEFARMVADRYRTNHFVDMVDSDDF-GLVDTLAAMYDEPYADSSAVPTYRVCQLARTH-VKV 360
                                           ****.********************99998888886.689999**************************.*** PP

                             TIGR01536 358 vLsGeGaDElfgGYeyfreakaeeale..................................lpeaselaekkl 396
                                           +LsG+G+DE fgGY ++r   +ee+++                                  +  +s++a+++ 
  NCBI__GCF_000430725.1:WP_029000198.1 361 ALSGDGGDEAFGGYRRYRMHMMEERMRsalplalrrplfgtlgrlypkadwapqvlrakttFEGMSRTAAQAY 433
                                           *****************************99999999999999999997776665555544333333333333 PP

                             TIGR01536 397 .....llqaklakeselkellkak.leeelkekeelkkelkeeseleellrldlelllsdllrak.Drvsmah 462
                                                +l++ l+++  +  l ++    ++l+ +e+++++  ++  l+ +++ dl+++l d+++ak Dr+sm h
  NCBI__GCF_000430725.1:WP_029000198.1 434 fhsmaRLRQPLRDRLFTGALKRELgGYSALEVFERHARRAGTDDPLALVQYIDLKTWLIDDINAKvDRASMEH 506
                                           333333333333333333333322022333444444444455599**************************** PP

                             TIGR01536 463 slEvRvPflDkelvelalsippelklrdgkeKvlLreaaeellPeeileRkKeaf 517
                                           +lEvR P++D+elve a+++p +lk+++g+ K+++++a+e  lP+++l+R+K++f
  NCBI__GCF_000430725.1:WP_029000198.1 507 GLEVREPLMDHELVEWAATLPSSLKVSAGEGKHVFKKALEPRLPHDVLYRPKMGF 561
                                           *****************************************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (647 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: 00:00:00.02
# Mc/sec: 13.53
//
[ok]

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

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Protein sequences (fasta format)
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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 2024 update 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 original 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