Alignments for a candidate for asnB in Azospirillum sp. B510

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Azospirillum sp. B510

Align Putative asparagine synthetase [glutamine-hydrolyzing]; EC 6.3.5.4 (characterized)
to candidate WP_012976121.1 AZL_RS19060 asparagine synthase (glutamine-hydrolyzing)

Query= SwissProt::P64248
         (652 letters)



>NCBI__GCF_000010725.1:WP_012976121.1
          Length = 684

 Score =  218 bits (555), Expect = 7e-61
 Identities = 179/596 (30%), Positives = 270/596 (45%), Gaps = 50/596 (8%)

Query: 1   MCGLLAFVAAPAGAAGPEGADAASAIARASHLMRHRGPDESGTWHAVDGASGGVVFGFNR 60
           MCG+   +A     A P G D    + R   ++ HRGPD  G +         +     R
Sbjct: 1   MCGVAGVLAG--SRAEPAGLDE---LKRMIAMLSHRGPDGYGFYR-----DDRIGLAHAR 50

Query: 61  LSIIDIAHSHQPLRWGPPEAPDRYVLV-FNGEIYNYLELRDELRTQHGAVFATDGDGEAI 119
           LSI+ +A   QP+        DR + + FNGEI+N++ELR +L  + G  F T  D E I
Sbjct: 51  LSIVGLAGGFQPIH-----NEDRSLWISFNGEIFNHVELRRDLEAR-GHRFYTRTDTEVI 104

Query: 120 LAGYHHWGTEVLQRLRGMFAFALWDTVTRELFCARDPFGIKPLFIATGAGGTAVASEKKC 179
           +  +  +G     RL G FA  LWD   REL+  RD  GI PLF A        ASE K 
Sbjct: 105 VHAFEEYGPATWARLNGQFAICLWDATRRELWLVRDRLGILPLFYARRGDHLVFASEAKA 164

Query: 180 LLDLVELVGFDTEIDH-RALQHYTVLQYVPEPETLHRGVRRLESGCFARIRADQLAPVIT 238
           L     +       DH R  Q +T     P      R V  + +    R+ +  LA  + 
Sbjct: 165 LFGGGRVA---PAFDHARLAQVFTHWSAAPHGSVFER-VESVPAATAIRVDS-TLALHVD 219

Query: 239 RYFVPRFAASP-ITNDNDQARYDEITAVLEDSVAKHMRADVTVGAFLSGGIDSTAIAALA 297
           RY+ P F A P +   +     D +   L D++   +RADV VG ++SGG+DS+ IAALA
Sbjct: 220 RYWQPDFTADPALAKLSLDEAADRLEEKLLDAIRLRLRADVPVGVYISGGLDSSVIAALA 279

Query: 298 IR-HNPRLITFTTGFEREGFSEIDVAVASAEAIGARHIAKVVSADEFVAALPEIVWYLDE 356
            +     + +F   F   GF E       A  +G  H   +    +  AALP++V + + 
Sbjct: 280 RKLDTTSMHSFGVRFTDAGFDETPQQRLVAGHVGTGHHDILCGPRDIQAALPDVVRHSET 339

Query: 357 PVADPALVPLFFVAREARKH-VKVVLSGEGADELFGGYTIYREPLSLRPFDYLP------ 409
           P+   A  PLF ++R  R+  ++VVLSGEGADE   GY +++E    R +   P      
Sbjct: 340 PLVRTAPAPLFLLSRLVRESGIRVVLSGEGADEWLAGYDLFKEDKVRRFWARQPGSKVRP 399

Query: 410 ------KPLRRSMGKVSKPLPEGMRGKSLLHRGSLTLEERYYGNARSFSGAQLREVLPGF 463
                  P     G+   PL      ++   RG +  +E +Y +   +      + L   
Sbjct: 400 KLLGRVHPFAAVNGQKDSPL-----WQAFFKRGMMETDEAFYAHRTRWRNTAWAQRLLSA 454

Query: 464 RPDWTHTDVTAPVYAES------AGWDPVARMQHIDLFTWLRGDIL-VKADKITMANSLE 516
               T  D     +  +      + W P+AR Q  ++ +++   +L  + D++ MAN +E
Sbjct: 455 DVQATADDAAFEAHVAAHLPDGWSRWSPLARSQWAEISSFMTPYLLSTQGDRVAMANGIE 514

Query: 517 LRVPFLDPEVFAVASRLPAGAKITRTTTKYALRRALEPIVPAHVLHRPKLGFPVPI 572
           +R PFLDP V  + + LP   K+     K ALRR     +PA ++ RPK  +  P+
Sbjct: 515 VRYPFLDPAVDDLCAALPDRVKMLGLRDKLALRRLAARHLPAEIVQRPKRPYRAPM 570


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: 1182
Number of extensions: 68
Number of successful extensions: 6
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: 684
Length adjustment: 38
Effective length of query: 614
Effective length of database: 646
Effective search space:   396644
Effective search space used:   396644
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_012976121.1 AZL_RS19060 (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.1938460.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.7e-143  465.3   0.0     2e-143  465.0   0.0    1.0  1  NCBI__GCF_000010725.1:WP_012976121.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000010725.1:WP_012976121.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  465.0   0.0    2e-143    2e-143       1     517 []       2     566 ..       2     566 .. 0.93

  Alignments for each domain:
  == domain 1  score: 465.0 bits;  conditional E-value: 2e-143
                             TIGR01536   1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlsegaQPlsnek.evv 72 
                                           Cg+ag+++ +++     +++k+m+ +l+hRGPD+ g+++d   ++ +l+h+RL+i+ l +g QP++ne+ + +
  NCBI__GCF_000010725.1:WP_012976121.1   2 CGVAGVLAGSRAEPAGLDELKRMIAMLSHRGPDGYGFYRD---DRIGLAHARLSIVGLAGGFQPIHNEDrSLW 71 
                                           *********99877799***********************...8**************************9** PP

                             TIGR01536  73 ivfnGEIYNheeLreeleekGyeFetksDtEViLaayeewgeelverLeGmFAfalwdekkgelflaRDrlGi 145
                                           i fnGEI+Nh eLr++le++G++F t++DtEVi++a+ee+g ++ +rL+G+FA+ lwd+ ++el l+RDrlGi
  NCBI__GCF_000010725.1:WP_012976121.1  72 ISFNGEIFNHVELRRDLEARGHRFYTRTDTEVIVHAFEEYGPATWARLNGQFAICLWDATRRELWLVRDRLGI 144
                                           ************************************************************************* PP

                             TIGR01536 146 kPLYyaseqgkllfaSEiKallalkeikaeldkealaelltlqlvptektlfkevkelepakal..dgeekle 216
                                            PL+ya+ +++l+faSE+Kal+   ++++++d++ la+++t+++ +++ ++f++v+ +++a a   d   +l+
  NCBI__GCF_000010725.1:WP_012976121.1 145 LPLFYARRGDHLVFASEAKALFGGGRVAPAFDHARLAQVFTHWSAAPHGSVFERVESVPAATAIrvD--STLA 215
                                           *******************************************9999***************99552..4333 PP

                             TIGR01536 217 e....ywevekee....vkeseeelveelrelledavkkrlvadvpvgvllSGGlDSslvaaiakkeaksevk 281
                                                yw+ + ++     k s++e+ ++l+e+l da++ rl+advpvgv++SGGlDSs++aa+a+k   ++++
  NCBI__GCF_000010725.1:WP_012976121.1 216 LhvdrYWQPDFTAdpalAKLSLDEAADRLEEKLLDAIRLRLRADVPVGVYISGGLDSSVIAALARKLDTTSMH 288
                                           33466****99999999999***************************************************** PP

                             TIGR01536 282 tFsigfedskdldeskaarkvadelgtehkevliseeevlkeleevilaleeptairasiplyllsklarekg 354
                                           +F ++f+ ++ +de+ ++r va ++gt h+ +l  + ++ ++l++v+++ e p+  +a +pl+lls+l+re g
  NCBI__GCF_000010725.1:WP_012976121.1 289 SFGVRFT-DAGFDETPQQRLVAGHVGTGHHDILCGPRDIQAALPDVVRHSETPLVRTAPAPLFLLSRLVRESG 360
                                           *******.***************************************************************** PP

                             TIGR01536 355 vkVvLsGeGaDElfgGYeyfreakaeeale..................................lpeaselae 393
                                           ++VvLsGeGaDE ++GY+ f+e k+++ +                                      ++e+ e
  NCBI__GCF_000010725.1:WP_012976121.1 361 IRVVLSGEGADEWLAGYDLFKEDKVRRFWArqpgskvrpkllgrvhpfaavngqkdsplwqaffKRGMMETDE 433
                                           *****************************99999999999988888877777777766665553223333555 PP

                             TIGR01536 394 kklllqaklakeselkellkakleeelkekeelkkelkee.......seleellrldlelllsdllrak..Dr 457
                                           +  +++++++++   ++ll+a+++++      +++  ++        s l++ + +++  +++ +l+    Dr
  NCBI__GCF_000010725.1:WP_012976121.1 434 AFYAHRTRWRNTAWAQRLLSADVQATADDAAFEAHVAAHLpdgwsrwSPLARSQWAEISSFMTPYLLSTqgDR 506
                                           55599999****99*****99999887765544444444466799999**************99998888*** PP

                             TIGR01536 458 vsmahslEvRvPflDkelvelalsippelklrdgkeKvlLreaaeellPeeileRkKeaf 517
                                           v+ma+++EvR+PflD ++ +l++ +p  +k+   + K  Lr++a+++lP ei++R+K+++
  NCBI__GCF_000010725.1:WP_012976121.1 507 VAMANGIEVRYPFLDPAVDDLCAALPDRVKMLGLRDKLALRRLAARHLPAEIVQRPKRPY 566
                                           *********************************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (684 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: 25.56
//
[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