Alignments for a candidate for tpi in Shewanella oneidensis MR-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for tpi in Shewanella oneidensis MR-1

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate 200380 SO1200 triosephosphate isomerase (NCBI ptt file)

Query= BRENDA::P0A858
         (255 letters)



>FitnessBrowser__MR1:200380
          Length = 260

 Score =  246 bits (627), Expect = 4e-70
 Identities = 124/259 (47%), Positives = 172/259 (66%), Gaps = 8/259 (3%)

Query: 1   MRHPLVMGNWKLNGSRHMVHELVSNLRKELAGVAGCAVAIAPPEMYIDM------AKREA 54
           +R P+V GNWK+NGS  +  EL      +L   +   V + PP +Y++       A +EA
Sbjct: 3   LRRPMVAGNWKMNGSAALAQELFKKFASKLQNDSA-EVVLCPPSIYLESVRQLLEANKEA 61

Query: 55  -EGSHIMLGAQNVDLNLSGAFTGETSAAMLKDIGAQYIIIGHSERRTYHKESDELIAKKF 113
            +GS + +GAQN+  +  GA+TGE S  MLKD G +Y+IIGHSERR  + E+  ++A+KF
Sbjct: 62  LDGSLVRMGAQNLSQHDFGAYTGEVSGQMLKDCGCRYVIIGHSERRRMYGETSNIVAEKF 121

Query: 114 AVLKEQGLTPVLCIGETEAENEAGKTEEVCARQIDAVLKTQGAAAFEGAVIAYEPVWAIG 173
           A  ++ GLTP+LC+GE+    EA +T EV A ++D V++  G  AF+ A+IAYEP+WA+G
Sbjct: 122 AAAQKHGLTPILCVGESGPAREARRTFEVIAEELDIVIQKNGTMAFDNAIIAYEPLWAVG 181

Query: 174 TGKSATPAQAQAVHKFIRDHIAKVDANIAEQVIIQYGGSVNASNAAELFAQPDIDGALVG 233
           TGKSATP QAQ VH FIR  +++V   I E + I YGGSV  SNAA+LFAQPD+DG L+G
Sbjct: 182 TGKSATPEQAQEVHAFIRKRLSEVSPFIGENIRILYGGSVTPSNAADLFAQPDVDGGLIG 241

Query: 234 GASLKADAFAVIVKAAEAA 252
           GASL +  F  +   A +A
Sbjct: 242 GASLNSTEFLSLCTIAMSA 260


Lambda     K      H
   0.316    0.130    0.366 

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: 202
Number of extensions: 9
Number of successful extensions: 2
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: 255
Length of database: 260
Length adjustment: 24
Effective length of query: 231
Effective length of database: 236
Effective search space:    54516
Effective search space used:    54516
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: 47 (22.7 bits)

Align candidate 200380 SO1200 (triosephosphate isomerase (NCBI ptt file))
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.carbon/TIGR00419.hmm
# target sequence database:        /tmp/gapView.20907.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
    4.5e-69  218.8   0.0    5.4e-69  218.5   0.0    1.1  1  lcl|FitnessBrowser__MR1:200380  SO1200 triosephosphate isomerase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:200380  SO1200 triosephosphate isomerase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  218.5   0.0   5.4e-69   5.4e-69       1     226 [.       7     246 ..       7     248 .. 0.92

  Alignments for each domain:
  == domain 1  score: 218.5 bits;  conditional E-value: 5.4e-69
                       TIGR00419   1 lviinfKlnesvgkvelevaklaeevaseagvevavappfvdldvvkdevese........iqvaAqnvdavksGaftG 71 
                                     +v +n+K+n+s    +++  k a ++ + +  ev++ pp ++l+ v++ +e++        ++++Aqn+  +++Ga+tG
  lcl|FitnessBrowser__MR1:200380   7 MVAGNWKMNGSAALAQELFKKFASKLQN-DSAEVVLCPPSIYLESVRQLLEANkealdgslVRMGAQNLSQHDFGAYTG 84 
                                     699**********************976.66899*********99976544221233333399**************** PP

                       TIGR00419  72 eisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleere.......aartinnvattaa 143
                                     e+s +mlkd+G+++v+igHsErR +  e+++++++k+a +++ gl++++Cvge+   re        a++++ v ++++
  lcl|FitnessBrowser__MR1:200380  85 EVSGQMLKDCGCRYVIIGHSERRRMYGETSNIVAEKFAAAQKHGLTPILCVGESGPAREarrtfevIAEELDIVIQKNG 163
                                     ******************************************************9999977778777888888999999 PP

                       TIGR00419 144 aaAlepdvvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvlyGasvtaaedaelaaqldvdGvLlas 222
                                     ++A++++++A+EP +++GtGk++++ +a++v++++r  l++vs+ + e++r+lyG+svt +++a+l+aq+dvdG L+++
  lcl|FitnessBrowser__MR1:200380 164 TMAFDNAIIAYEPLWAVGTGKSATPEQAQEVHAFIRKRLSEVSPFIGENIRILYGGSVTPSNAADLFAQPDVDGGLIGG 242
                                     99***************************************************************************** PP

                       TIGR00419 223 avlk 226
                                     a+l 
  lcl|FitnessBrowser__MR1:200380 243 ASLN 246
                                     *996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (228 nodes)
Target sequences:                          1  (260 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: 6.42
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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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

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 catabolism of small carbon sources