Alignments for a candidate for trpE in Azohydromonas australica DSM 1124

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpE in Azohydromonas australica DSM 1124

Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (characterized)
to candidate WP_028997307.1 H537_RS0106860 anthranilate synthase component I

Query= SwissProt::P20579
         (493 letters)



>NCBI__GCF_000430725.1:WP_028997307.1
          Length = 491

 Score =  523 bits (1346), Expect = e-153
 Identities = 274/493 (55%), Positives = 351/493 (71%), Gaps = 17/493 (3%)

Query: 5   EFLRLAAVGYNRIPLACETLADFDTPLSIYLKLAD-QPNSYLLESVQGGEKWGRYSMIGL 63
           EF  LAA G+NRIPL  E  AD +TPLS+YLKLA  +PNS+LLESV GGE++GRYS IGL
Sbjct: 6   EFKSLAAEGFNRIPLIAEAFADLETPLSLYLKLAGGRPNSFLLESVVGGERFGRYSFIGL 65

Query: 64  PSRTVMRVHGYHVSILHDGVEVESHDVEDPLAFVESFKDRYKVADIPGLPRFNGGLVGYF 123
           P+RT++R  G    I+ DG  VESH+  +PL F+ +++ R+K    PGLPRF GGL GYF
Sbjct: 66  PARTLLRATGQKTEIVTDGQVVESHE-GNPLDFIAAYQQRFKPVLRPGLPRFCGGLAGYF 124

Query: 124 GYDCVRYVEKRLGVSPNPDPLGVPDILLMVSDAVVVFDNLAGKMHAIVLVDPAEEQAFEQ 183
           GYD VR++E +L  +     +G PDILL+ ++ V V DNL+G+++ IV  DPA+ +++ +
Sbjct: 125 GYDAVRFMESKLARTVKEGGIGTPDILLLQTEEVAVIDNLSGRLYLIVWADPAQAESYFR 184

Query: 184 GQARLQGLLETLRQPITP---RRGLDLSGPQAAEPEFRSSYTREDYENAVGRIKEYILAG 240
            + RL  L + LR  ++    RRG         E EF     + D+E AV R KEYI AG
Sbjct: 185 AKKRLTELTDQLRYSVSAPAVRRGQSYP----VEREF----AKADFEAAVLRCKEYIAAG 236

Query: 241 DCMQVVPSQRMSIDFKAAPIDLYRALRCFNPTPYMYFFNFGDFHVVGSSPEVLVR----V 296
           DCMQVV  QR+   +  +P+ LYRALR  NP+PYMYF++ G+F +VGSSPE+LVR     
Sbjct: 237 DCMQVVLGQRLKKRYTESPLSLYRALRSLNPSPYMYFYDLGEFQIVGSSPEILVRHEHVA 296

Query: 297 EDNLVTVRPIAGTRPRGATEEADRALEDDLLSDDKEIAEHLMLIDLGRNDVGRVSSTGSV 356
           E   VT+RP+AGTRPRGAT E D A E +LL+D KE AEHLMLIDL RND+GR++ TGSV
Sbjct: 297 EGEKVTIRPLAGTRPRGATPEKDAANETELLADPKERAEHLMLIDLARNDIGRIAQTGSV 356

Query: 357 RLTEKMVIERYSNVMHIVSNVAGQLREGLTAMDALRAILPAGTLSGAPKIRAMEIIDELE 416
           ++TE   +ERYS+VMHIVSNV G L+ G   +D LRA  PAGTLSGAPKIRAMEIIDELE
Sbjct: 357 KVTEAFAVERYSHVMHIVSNVEGLLKPGTNNLDVLRATFPAGTLSGAPKIRAMEIIDELE 416

Query: 417 PVKRGVYGGAVGYFAWNGNMDTAIAIRTAVINDGELHVQAGGGIVADSVPALEWEETINK 476
           PV+RG+YGGA GY ++ G+MD AIAIRT ++ D  L+VQA  G+VADSVP +EW+ET  K
Sbjct: 417 PVQRGIYGGACGYLSFAGDMDVAIAIRTGIVKDQVLYVQAAAGVVADSVPEMEWKETEAK 476

Query: 477 RRAMFRAVALAEQ 489
            RA+ RA  L E+
Sbjct: 477 ARAVLRAAELVEE 489


Lambda     K      H
   0.320    0.138    0.403 

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: 691
Number of extensions: 34
Number of successful extensions: 5
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: 493
Length of database: 491
Length adjustment: 34
Effective length of query: 459
Effective length of database: 457
Effective search space:   209763
Effective search space used:   209763
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.6 bits)

Align candidate WP_028997307.1 H537_RS0106860 (anthranilate synthase component I)
to HMM TIGR00564 (trpE: anthranilate synthase component I (EC 4.1.3.27))

# 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/TIGR00564.hmm
# target sequence database:        /tmp/gapView.24834.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00564  [M=455]
Accession:   TIGR00564
Description: trpE_most: anthranilate synthase component I
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.8e-167  543.9   0.0     2e-167  543.7   0.0    1.0  1  lcl|NCBI__GCF_000430725.1:WP_028997307.1  H537_RS0106860 anthranilate synt


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000430725.1:WP_028997307.1  H537_RS0106860 anthranilate synthase component I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  543.7   0.0    2e-167    2e-167       1     454 [.      26     484 ..      26     485 .. 0.94

  Alignments for each domain:
  == domain 1  score: 543.7 bits;  conditional E-value: 2e-167
                                 TIGR00564   1 adtltpisvylklak.rkesfllEsvekeeelgRySliglnpvleikakdgkavlleaddeeakieede 68 
                                               ad +tp+s+ylkla  r++sfllEsv  +e+ gRyS+igl  ++ ++a+++k+++++  +  +++e+++
  lcl|NCBI__GCF_000430725.1:WP_028997307.1  26 ADLETPLSLYLKLAGgRPNSFLLESVVGGERFGRYSFIGLPARTLLRATGQKTEIVTDGQVVESHEGNP 94 
                                               5889***********99***********************9999999998866666655555569**** PP

                                 TIGR00564  69 lkelrklleka.eesedeldeplsggavGylgydtvrlveklkeea..edelelpdlllllvetvivfD 134
                                               l+ + +  +++    +++l+  ++gg+ Gy+gyd vr++e++ +++  e  + +pd+lll +e+v+v D
  lcl|NCBI__GCF_000430725.1:WP_028997307.1  95 LDFIAAYQQRFkPVLRPGLPR-FCGGLAGYFGYDAVRFMESKLARTvkEGGIGTPDILLLQTEEVAVID 162
                                               **********98788999987.******************99886543677999*************** PP

                                 TIGR00564 135 hvekkvilienarteaersaeeeaaarleellaelqkelekavkaleekkesftsnvekeeyeekvaka 203
                                               + + +++li +a  ++ + ++  a++rl+el+ +l+ +++    +   ++++++ ++ k+++e++v + 
  lcl|NCBI__GCF_000430725.1:WP_028997307.1 163 NLSGRLYLIVWADPAQAE-SYFRAKKRLTELTDQLRYSVSA-PAVRRGQSYPVEREFAKADFEAAVLRC 229
                                               ************877777.788999***********99974.44556677889**************** PP

                                 TIGR00564 204 keyikaGdifqvvlSqrleakveakpfelYrkLRtvNPSpylyyldledfelvgsSPEllvkvk....g 268
                                               keyi+aGd +qvvl qrl+++ + +p++lYr+LR+ NPSpy+y+ dl +f++vgsSPE+lv+ +    g
  lcl|NCBI__GCF_000430725.1:WP_028997307.1 230 KEYIAAGDCMQVVLGQRLKKRYTESPLSLYRALRSLNPSPYMYFYDLGEFQIVGSSPEILVRHEhvaeG 298
                                               *************************************************************98888878 PP

                                 TIGR00564 269 krvetrPiAGtrkRGatkeeDealeeeLladeKerAEHlmLvDLaRNDigkvaklgsvevkellkieky 337
                                               ++v++rP+AGtr+RGat+e+D+a+e+eLlad+KerAEHlmL+DLaRNDig++a++gsv+v+e + +e+y
  lcl|NCBI__GCF_000430725.1:WP_028997307.1 299 EKVTIRPLAGTRPRGATPEKDAANETELLADPKERAEHLMLIDLARNDIGRIAQTGSVKVTEAFAVERY 367
                                               88******************************************************************* PP

                                 TIGR00564 338 shvmHivSeVeGelkdeltavDalraalPaGTlsGAPKvrAmelidelEkekRgiYgGavgylsfdgdv 406
                                               shvmHivS+VeG lk++++++D+lra++PaGTlsGAPK+rAme+idelE+++RgiYgGa gylsf+gd+
  lcl|NCBI__GCF_000430725.1:WP_028997307.1 368 SHVMHIVSNVEGLLKPGTNNLDVLRATFPAGTLSGAPKIRAMEIIDELEPVQRGIYGGACGYLSFAGDM 436
                                               ********************************************************************* PP

                                 TIGR00564 407 dtaiaiRtmvlkdgvayvqAgaGiVaDSdpeaEyeEtlnKakallrai 454
                                               d+aiaiRt ++kd+v+yvqA+aG+VaDS+pe E++Et  Ka+a+lra+
  lcl|NCBI__GCF_000430725.1:WP_028997307.1 437 DVAIAIRTGIVKDQVLYVQAAAGVVADSVPEMEWKETEAKARAVLRAA 484
                                               *********************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (491 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: 10.84
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 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