Alignments for a candidate for tpiA in Chlorobium phaeobacteroides BS1

GapMind for Amino acid biosynthesis

Alignments for a candidate for tpiA in Chlorobium phaeobacteroides BS1

Align Triosephosphate isomerase; TIM; TPI; Triose-phosphate isomerase; EC 5.3.1.1 (characterized)
to candidate WP_012474341.1 CPHAMN1_RS04525 triose-phosphate isomerase

Query= SwissProt::Q8XKU1
         (248 letters)



>NCBI__GCF_000020545.1:WP_012474341.1
          Length = 250

 Score =  236 bits (603), Expect = 2e-67
 Identities = 117/249 (46%), Positives = 166/249 (66%), Gaps = 4/249 (1%)

Query: 1   MRTPIIAGNWKMHYTIDEAVKLVEELKPLVKDAK--CEVVVCPTFVCLDAVKKAVEGTNI 58
           MR  I+ GNWKM+  + E V L   +   +   K  CEV + P +  L  V + +EG++I
Sbjct: 1   MRKKIVVGNWKMNKNVAEGVALASSILENLDGGKMACEVGIAPAYPVLSEVGRVIEGSDI 60

Query: 59  KVGAQNMHFEEKGAFTGEIAPRMLEAMNIDYVIIGHSERREYFNETDETCNKKVKAAFAH 118
            + AQN H+E++GA+TGE++ RML+++   Y+I+GHSERR+YF ET+ T N ++K A   
Sbjct: 61  CLVAQNCHYEDEGAYTGEVSVRMLDSLGCSYIIVGHSERRQYFGETNRTVNLRLKKALEG 120

Query: 119 NLTPILCCGETLEQRENGTTNDVIKAQITADLEGLTKEQAEKVVIAYEPIWAIGTGKTAT 178
            +  ILC GETLE+RE G T+ ++ AQ+   L  +  E    VV+AYEP+WAIGTGKTAT
Sbjct: 121 GMRVILCIGETLEEREAGVTDAIVTAQVREGLADI--EDLGNVVLAYEPVWAIGTGKTAT 178

Query: 179 SDQANETIAAIRAMVAEMFGQEVADKVRIQYGGSVKPNTIAEQMAKSDIDGALVGGASLV 238
            +QA+   A+IRA +++M+G+  A+ +RIQYGGSVKP+   E     +IDG L+GGASL 
Sbjct: 179 PEQADAVHASIRATISDMYGEADAEDIRIQYGGSVKPSNAVELFGMPNIDGGLIGGASLK 238

Query: 239 AADFAQIVN 247
           A DF  IVN
Sbjct: 239 ADDFVAIVN 247


Lambda     K      H
   0.316    0.131    0.376 

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: 175
Number of extensions: 6
Number of successful extensions: 3
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: 248
Length of database: 250
Length adjustment: 24
Effective length of query: 224
Effective length of database: 226
Effective search space:    50624
Effective search space used:    50624
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 46 (22.3 bits)

Align candidate WP_012474341.1 CPHAMN1_RS04525 (triose-phosphate isomerase)
to HMM TIGR00419 (tpiA: triose-phosphate isomerase (EC 5.3.1.1))

# 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/TIGR00419.hmm
# target sequence database:        /tmp/gapView.28514.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00419  [M=228]
Accession:   TIGR00419
Description: tim: triose-phosphate isomerase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    6.8e-65  205.1   0.9    7.7e-65  204.9   0.9    1.0  1  lcl|NCBI__GCF_000020545.1:WP_012474341.1  CPHAMN1_RS04525 triose-phosphate


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000020545.1:WP_012474341.1  CPHAMN1_RS04525 triose-phosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  204.9   0.9   7.7e-65   7.7e-65       1     228 []       5     240 ..       5     240 .. 0.93

  Alignments for each domain:
  == domain 1  score: 204.9 bits;  conditional E-value: 7.7e-65
                                 TIGR00419   1 lviinfKlnesvgkvelevaklaeeva.seagvevavappfvdldvvkdeve.seiqvaAqnvdavksG 67 
                                               +v++n+K+n  v +   + +++ e++  ++  +ev++ap +  l+ v + +e s+i ++Aqn++  + G
  lcl|NCBI__GCF_000020545.1:WP_012474341.1   5 IVVGNWKMNKNVAEGVALASSILENLDgGKMACEVGIAPAYPVLSEVGRVIEgSDICLVAQNCHYEDEG 73 
                                               79**********************99626889************************************* PP

                                 TIGR00419  68 aftGeisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartin 136
                                               a+tGe+s  ml  lG+ ++++gHsErR ++ e++  ++ ++ ++ e g+++++C+getleerea+ t  
  lcl|NCBI__GCF_000020545.1:WP_012474341.1  74 AYTGEVSVRMLDSLGCSYIIVGHSERRQYFGETNRTVNLRLKKALEGGMRVILCIGETLEEREAGVTDA 142
                                               ***************************************************************999865 PP

                                 TIGR00419 137 nvatt.aaaaA....lepdvvAvEPveliGtGkpvskAeaevveksvrdhlkkvskev.aesvrvlyGa 199
                                                v+ + ++  A    l ++v+A+EPv++iGtGk++++ +a++v++s+r  ++    e  ae++r++yG+
  lcl|NCBI__GCF_000020545.1:WP_012474341.1 143 IVTAQvREGLAdiedLGNVVLAYEPVWAIGTGKTATPEQADAVHASIRATISDMYGEAdAEDIRIQYGG 211
                                               555442344557889************************************9965554389******** PP

                                 TIGR00419 200 svtaaedaelaaqldvdGvLlasavlkae 228
                                               sv+ ++++el+  +++dG L+++a+lka+
  lcl|NCBI__GCF_000020545.1:WP_012474341.1 212 SVKPSNAVELFGMPNIDGGLIGGASLKAD 240
                                               ***************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (228 nodes)
Target sequences:                          1  (250 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 6.62
//
[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