Alignments for a candidate for trpE in Herbaspirillum seropedicae SmR1

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpE in Herbaspirillum seropedicae SmR1

Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (characterized)
to candidate HSERO_RS19435 HSERO_RS19435 anthranilate synthase subunit I

Query= SwissProt::P20579
         (493 letters)



>FitnessBrowser__HerbieS:HSERO_RS19435
          Length = 498

 Score =  519 bits (1336), Expect = e-151
 Identities = 266/492 (54%), Positives = 348/492 (70%), Gaps = 15/492 (3%)

Query: 1   MNREEFLRLAAVGYNRIPLACETLADFDTPLSIYLKLADQ----PNSYLLESVQGGEKWG 56
           M   EF  LA  GYNRIPL  E  AD +TPL++YLKLA       N++LLESV GGE++G
Sbjct: 1   MTELEFKSLATEGYNRIPLIAEAFADLETPLTLYLKLAQSHHTGKNTFLLESVVGGERFG 60

Query: 57  RYSMIGLPSRTVMRVHGYHVSILHDGVEVESHDVEDPLAFVESFKDRYKVADIPGLPRFN 116
           RYS IGLP+ T +R  G  + +L + V +E+ +  + L F+  ++ R+KVA  PG+PRF 
Sbjct: 61  RYSFIGLPASTKIRCSGKQIEVLKNDVVIETAE-GNALEFIAQYQSRFKVAIRPGMPRFC 119

Query: 117 GGLVGYFGYDCVRYVEKRLGVSPNPDPLGVPDILLMVSDAVVVFDNLAGKMHAIVLVDPA 176
           GGL GYFGYD VRY+EKRL  S   D LG+PDI L++++ + V DNL+GK++ IV  DP 
Sbjct: 120 GGLAGYFGYDAVRYIEKRLEDSAPKDTLGLPDIQLLLTEELAVIDNLSGKLYLIVYADPT 179

Query: 177 EEQAFEQGQARLQGLLETLRQPITPRRGLDLSGPQAAEPEFRSSYTREDYENAVGRIKEY 236
           + +AF +G+ RL+ L   LR+P             +   E    + +++Y  AV R KEY
Sbjct: 180 QPEAFSRGRQRLRDLRAMLRRPADAPVTTG-----SVRTETIREFPKDEYLKAVARAKEY 234

Query: 237 ILAGDCMQVVPSQRMSIDFKAAPIDLYRALRCFNPTPYMYFFNFGDFHVVGSSPEVLVRV 296
           ++AGD MQV   QR+   +  +P+ LYRALR  NP+PYMYF+NFGD  +VG+SPE+LVR 
Sbjct: 235 VMAGDLMQVQIGQRLKKSYVDSPLMLYRALRSLNPSPYMYFYNFGDMQIVGASPEILVRN 294

Query: 297 ED-----NLVTVRPIAGTRPRGATEEADRALEDDLLSDDKEIAEHLMLIDLGRNDVGRVS 351
           E        +T+RP+AGTRPRG+T E D  L  +LL+D KEIAEH+MLIDL RND+GR++
Sbjct: 295 ESIGEGQKKITIRPLAGTRPRGSTIERDEQLARELLADPKEIAEHVMLIDLARNDIGRIA 354

Query: 352 STGSVRLTEKMVIERYSNVMHIVSNVAGQLREGLTAMDALRAILPAGTLSGAPKIRAMEI 411
           +TGSV++T++MVIE+YS+V HIVSNV G L+ G++ +D L+A  PAGTLSGAPK+RAMEI
Sbjct: 355 TTGSVKVTDQMVIEKYSHVQHIVSNVEGILKPGMSNLDVLKATFPAGTLSGAPKVRAMEI 414

Query: 412 IDELEPVKRGVYGGAVGYFAWNGNMDTAIAIRTAVINDGELHVQAGGGIVADSVPALEWE 471
           IDELEP KRG+YGGA GY ++ G MD AIAIRT VI DG L+VQA  GIVADSVP +EWE
Sbjct: 415 IDELEPTKRGIYGGACGYLSFGGEMDVAIAIRTGVIKDGTLYVQAAAGIVADSVPEMEWE 474

Query: 472 ETINKRRAMFRA 483
           ET NK RA+ RA
Sbjct: 475 ETENKARAVLRA 486


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: 660
Number of extensions: 28
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: 498
Length adjustment: 34
Effective length of query: 459
Effective length of database: 464
Effective search space:   212976
Effective search space used:   212976
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 HSERO_RS19435 HSERO_RS19435 (anthranilate synthase subunit 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.3031.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   5.7e-169  548.8   0.0   6.5e-169  548.6   0.0    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS19435  HSERO_RS19435 anthranilate synth


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS19435  HSERO_RS19435 anthranilate synthase subunit I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  548.6   0.0  6.5e-169  6.5e-169       1     454 [.      25     487 ..      25     488 .. 0.95

  Alignments for each domain:
  == domain 1  score: 548.6 bits;  conditional E-value: 6.5e-169
                                  TIGR00564   1 adtltpisvylklak.r...kesfllEsvekeeelgRySliglnpvleikakdgkavlleaddeeaki 64 
                                                ad +tp+++ylkla+ +   k++fllEsv  +e+ gRyS+igl   ++i++++++++ l++d   ++ 
  lcl|FitnessBrowser__HerbieS:HSERO_RS19435  25 ADLETPLTLYLKLAQsHhtgKNTFLLESVVGGERFGRYSFIGLPASTKIRCSGKQIEVLKNDVVIETA 92 
                                                5889**********95489999**********************************999999999999 PP

                                  TIGR00564  65 eedelkelrkllekaeesedeldeplsggavGylgydtvrlveklke.ea.edelelpdlllllvetv 130
                                                e+++l+ + +  ++++  +    + ++gg+ Gy+gyd vr++ek  e +a +d+l lpd+ lll+e++
  lcl|FitnessBrowser__HerbieS:HSERO_RS19435  93 EGNALEFIAQYQSRFKVAIRPGMPRFCGGLAGYFGYDAVRYIEKRLEdSApKDTLGLPDIQLLLTEEL 160
                                                ***************7766655566******************98764446***************** PP

                                  TIGR00564 131 ivfDhvekkvilienarteaersaeeeaaarleellaelqkelekavkaleekkesftsnvekeeyee 198
                                                +v D+ + k++li +a  ++ + a++  ++rl++l a l++++   v++   ++e++  ++ k+ey +
  lcl|FitnessBrowser__HerbieS:HSERO_RS19435 161 AVIDNLSGKLYLIVYADPTQPE-AFSRGRQRLRDLRAMLRRPADAPVTTGSVRTETI-REFPKDEYLK 226
                                                ****************888777.9*******************98788776666655.99******** PP

                                  TIGR00564 199 kvakakeyikaGdifqvvlSqrleakveakpfelYrkLRtvNPSpylyyldledfelvgsSPEllvkv 266
                                                +va+akey+ aGd++qv++ qrl+++   +p+ lYr+LR+ NPSpy+y+ ++ d+++vg+SPE+lv+ 
  lcl|FitnessBrowser__HerbieS:HSERO_RS19435 227 AVARAKEYVMAGDLMQVQIGQRLKKSYVDSPLMLYRALRSLNPSPYMYFYNFGDMQIVGASPEILVRN 294
                                                *******************************************************************9 PP

                                  TIGR00564 267 k.....gkrvetrPiAGtrkRGatkeeDealeeeLladeKerAEHlmLvDLaRNDigkvaklgsvevk 329
                                                +     +k++++rP+AGtr+RG+t e De+l++eLlad+Ke AEH+mL+DLaRNDig++a++gsv+v+
  lcl|FitnessBrowser__HerbieS:HSERO_RS19435 295 EsigegQKKITIRPLAGTRPRGSTIERDEQLARELLADPKEIAEHVMLIDLARNDIGRIATTGSVKVT 362
                                                999884455*********************************************************** PP

                                  TIGR00564 330 ellkiekyshvmHivSeVeGelkdeltavDalraalPaGTlsGAPKvrAmelidelEkekRgiYgGav 397
                                                + + iekyshv+HivS+VeG lk++++++D+l+a++PaGTlsGAPKvrAme+idelE++kRgiYgGa 
  lcl|FitnessBrowser__HerbieS:HSERO_RS19435 363 DQMVIEKYSHVQHIVSNVEGILKPGMSNLDVLKATFPAGTLSGAPKVRAMEIIDELEPTKRGIYGGAC 430
                                                ******************************************************************** PP

                                  TIGR00564 398 gylsfdgdvdtaiaiRtmvlkdgvayvqAgaGiVaDSdpeaEyeEtlnKakallrai 454
                                                gylsf g++d+aiaiRt v+kdg++yvqA+aGiVaDS+pe E+eEt nKa+a+lra+
  lcl|FitnessBrowser__HerbieS:HSERO_RS19435 431 GYLSFGGEMDVAIAIRTGVIKDGTLYVQAAAGIVADSVPEMEWEETENKARAVLRAA 487
                                                ******************************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (498 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 10.35
//
[ok]

This GapMind analysis is from Apr 09 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