Alignments for a candidate for trpE in Rhodospirillum centenum SW SW; ATCC 51521

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpE in Rhodospirillum centenum SW SW; ATCC 51521

Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (characterized)
to candidate WP_012565349.1 RC1_RS00475 anthranilate synthase component I

Query= SwissProt::P20579
         (493 letters)



>NCBI__GCF_000016185.1:WP_012565349.1
          Length = 509

 Score =  421 bits (1083), Expect = e-122
 Identities = 234/481 (48%), Positives = 308/481 (64%), Gaps = 18/481 (3%)

Query: 24  LADFDTPLSIYLKLAD-QPNSYLLESVQGGEKWGRYSMIGLPSRTVMRVHGYHVSI---L 79
           ++D DTP+S  +KL+  +PN++LLESV GG   GRYS+IGL    + R  G    +    
Sbjct: 27  VSDLDTPVSAMMKLSQGRPNAFLLESVTGGSVRGRYSLIGLKPDLMWRSKGDRAEVNRRF 86

Query: 80  HDGVEVESHDVEDPLAFVESFKDRYKVADIPGLPRFNGGLVGYFGYDCVRYVEKRLGVSP 139
            +  E      E PL  + +  +  ++A    LP  + GL GY GYD VR +E+      
Sbjct: 87  AEAPEAFEPCPEPPLKALAALLEESRIALPASLPPMSAGLFGYLGYDMVRLMERL--PDA 144

Query: 140 NPDPLGVPDILLMVSDAVVVFDNLAGKMHAIVLVDPAEEQ-------AFEQGQARLQGLL 192
           NPD LG+ D +L+    + +FD +    + I +V P  ++       A+ +   RL   +
Sbjct: 145 NPDELGLDDAILIRPTVMAIFDGIE---NVITVVTPVRKEPGIDADVAYRRATERLAEAV 201

Query: 193 ETLRQPITPRRGLDLSGPQAAEPEFRSSYTREDYENAVGRIKEYILAGDCMQVVPSQRMS 252
             L  P+    G DL      EP   S+ +R +Y   V R KEYI AGD  QVVPSQR S
Sbjct: 202 ADLEGPVPAALGTDLDLQPLPEPA--SNTSRAEYHALVERAKEYIRAGDIFQVVPSQRFS 259

Query: 253 IDFKAAPIDLYRALRCFNPTPYMYFFNFGDFHVVGSSPEVLVRVEDNLVTVRPIAGTRPR 312
           + F   P  LYRALR  NP+P+++F +FG   VVGSSPE+LVR+ DN VT+RPIAGTR R
Sbjct: 260 VPFSLPPFALYRALRRLNPSPFLFFLDFGHVSVVGSSPEILVRLRDNTVTIRPIAGTRRR 319

Query: 313 GATEEADRALEDDLLSDDKEIAEHLMLIDLGRNDVGRVSSTGSVRLTEKMVIERYSNVMH 372
           G     D+ L  DLLSD KE+AEHLML+DLGRNDVGRV+  G+V++TE+  IE YS+VMH
Sbjct: 320 GKDAAEDKELAADLLSDPKELAEHLMLLDLGRNDVGRVAQVGTVKVTERFTIEYYSHVMH 379

Query: 373 IVSNVAGQLREGLTAMDALRAILPAGTLSGAPKIRAMEIIDELEPVKRGVYGGAVGYFAW 432
           IVSNV GQ+    TA+DAL A  PAGT+SGAPKIRAMEIIDELE  +RG+YGG +GYFA 
Sbjct: 380 IVSNVEGQVAPTFTAIDALIAGFPAGTVSGAPKIRAMEIIDELEKTRRGIYGGCIGYFAA 439

Query: 433 NGNMDTAIAIRTAVINDGELHVQAGGGIVADSVPALEWEETINKRRAMFRAVALAEQTSA 492
           NG MDT IA+RTAVI DG ++VQAGGG+VADS P  E++ET+NK +A+F+A   A + +A
Sbjct: 440 NGTMDTCIALRTAVIKDGMMYVQAGGGVVADSDPEAEYQETVNKSKALFKAAEEAMRFAA 499

Query: 493 K 493
           +
Sbjct: 500 E 500


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: 684
Number of extensions: 33
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: 509
Length adjustment: 34
Effective length of query: 459
Effective length of database: 475
Effective search space:   218025
Effective search space used:   218025
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_012565349.1 RC1_RS00475 (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.3582955.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.9e-178  579.4   0.0   3.4e-178  579.2   0.0    1.0  1  NCBI__GCF_000016185.1:WP_012565349.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000016185.1:WP_012565349.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  579.2   0.0  3.4e-178  3.4e-178       2     454 ..      29     491 ..      28     492 .. 0.94

  Alignments for each domain:
  == domain 1  score: 579.2 bits;  conditional E-value: 3.4e-178
                             TIGR00564   2 dtltpisvylklak.rkesfllEsvekeeelgRySliglnpvleikakdg.kavlleaddeeak...ieedel 69 
                                           d  tp+s++ kl++ r++ fllEsv+ ++ +gRySligl+p+l ++ k++  +v+ + ++  +      e +l
  NCBI__GCF_000016185.1:WP_012565349.1  29 DLDTPVSAMMKLSQgRPNAFLLESVTGGSVRGRYSLIGLKPDLMWRSKGDrAEVNRRFAEAPEAfepCPEPPL 101
                                           778***********99********************************9943333333333333457899999 PP

                             TIGR00564  70 kelrkllekaeesedeldeplsggavGylgydtvrlveklkeeaedelelpdlllllvetvivfDhvekkvil 142
                                           k+l +lle+ ++  +   +p+s+g++Gylgyd+vrl+e+l+++++del l+d++l+  + +++fD +e+ +++
  NCBI__GCF_000016185.1:WP_012565349.1 102 KALAALLEESRIALPASLPPMSAGLFGYLGYDMVRLMERLPDANPDELGLDDAILIRPTVMAIFDGIENVITV 174
                                           9999999998888877779****************************************************** PP

                             TIGR00564 143 ienarteaers...aeeeaaarleellaelqkeleka..vkaleekkesftsnvekeeyeekvakakeyikaG 210
                                           ++ +r+e + +   a++ a++rl e +a+l+ ++  a  ++   +   + +sn++++ey++ v++akeyi+aG
  NCBI__GCF_000016185.1:WP_012565349.1 175 VTPVRKEPGIDadvAYRRATERLAEAVADLEGPVPAAlgTDLDLQPLPEPASNTSRAEYHALVERAKEYIRAG 247
                                           ******999888889999****************98854444455556699********************** PP

                             TIGR00564 211 difqvvlSqrleakveakpfelYrkLRtvNPSpylyyldledfelvgsSPEllvkvkgkrvetrPiAGtrkRG 283
                                           difqvv+Sqr++++++++pf+lYr+LR+ NPSp+l++ld+  +++vgsSPE+lv++++++v++rPiAGtr+RG
  NCBI__GCF_000016185.1:WP_012565349.1 248 DIFQVVPSQRFSVPFSLPPFALYRALRRLNPSPFLFFLDFGHVSVVGSSPEILVRLRDNTVTIRPIAGTRRRG 320
                                           ************************************************************************* PP

                             TIGR00564 284 atkeeDealeeeLladeKerAEHlmLvDLaRNDigkvaklgsvevkellkiekyshvmHivSeVeGelkdelt 356
                                           ++ +eD+ l+++Ll+d+Ke AEHlmL+DL+RND+g+va++g+v+v+e ++ie yshvmHivS+VeG++++++t
  NCBI__GCF_000016185.1:WP_012565349.1 321 KDAAEDKELAADLLSDPKELAEHLMLLDLGRNDVGRVAQVGTVKVTERFTIEYYSHVMHIVSNVEGQVAPTFT 393
                                           ************************************************************************* PP

                             TIGR00564 357 avDalraalPaGTlsGAPKvrAmelidelEkekRgiYgGavgylsfdgdvdtaiaiRtmvlkdgvayvqAgaG 429
                                           a+Dal+a +PaGT+sGAPK+rAme+idelEk++RgiYgG++gy+ ++g++dt+ia+Rt+v+kdg++yvqAg+G
  NCBI__GCF_000016185.1:WP_012565349.1 394 AIDALIAGFPAGTVSGAPKIRAMEIIDELEKTRRGIYGGCIGYFAANGTMDTCIALRTAVIKDGMMYVQAGGG 466
                                           ************************************************************************* PP

                             TIGR00564 430 iVaDSdpeaEyeEtlnKakallrai 454
                                           +VaDSdpeaEy+Et+nK+kal +a+
  NCBI__GCF_000016185.1:WP_012565349.1 467 VVADSDPEAEYQETVNKSKALFKAA 491
                                           *********************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (509 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: 21.74
//
[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