GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tpi in Algiphilus aromaticivorans DG1253

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_043767302.1 U743_RS08580 triose-phosphate isomerase

Query= BRENDA::P0A858
         (255 letters)



>NCBI__GCF_000733765.1:WP_043767302.1
          Length = 254

 Score =  233 bits (595), Expect = 2e-66
 Identities = 129/251 (51%), Positives = 162/251 (64%), Gaps = 6/251 (2%)

Query: 2   RHPLVMGNWKLNGSRHMVHELVSNLRKELAGV--AGCAVAIAPPEMYIDMAKREAEGSHI 59
           R PLV  NWK++G R     L    R+ +A    AG  V I PP  Y+ +      GS  
Sbjct: 3   RKPLVAANWKMHGDRAFGEALA---RETVASCDDAGVDVVICPPICYLTLVAGPLSGSGC 59

Query: 60  MLGAQNVDLNL-SGAFTGETSAAMLKDIGAQYIIIGHSERRTYHKESDELIAKKFAVLKE 118
            LGAQ++   + SGA TG+ + AML D GA ++I+GHSERR    E +E +A KF   ++
Sbjct: 60  ALGAQDLSPVVESGAHTGDINGAMLIDCGASHVIVGHSERRATRGEDNEAVAAKFLAAQQ 119

Query: 119 QGLTPVLCIGETEAENEAGKTEEVCARQIDAVLKTQGAAAFEGAVIAYEPVWAIGTGKSA 178
            GLTP+LC+GET AE +  +TE V   Q+DAV+   G AAF  AVIAYEPVWAIGTG++A
Sbjct: 120 AGLTPILCVGETLAERDGERTEAVLEAQLDAVVAAAGIAAFSRAVIAYEPVWAIGTGRTA 179

Query: 179 TPAQAQAVHKFIRDHIAKVDANIAEQVIIQYGGSVNASNAAELFAQPDIDGALVGGASLK 238
           +P QAQA H  +R  +A+ DA IA+ V I YGGSV   NAA LFAQPD+DG L+GGASLK
Sbjct: 180 SPDQAQAAHAALRATLARDDARIADSVRIVYGGSVKPDNAASLFAQPDVDGGLIGGASLK 239

Query: 239 ADAFAVIVKAA 249
           A  FA IV AA
Sbjct: 240 AADFAAIVHAA 250


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: 198
Number of extensions: 9
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: 255
Length of database: 254
Length adjustment: 24
Effective length of query: 231
Effective length of database: 230
Effective search space:    53130
Effective search space used:    53130
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 WP_043767302.1 U743_RS08580 (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.carbon/TIGR00419.hmm
# target sequence database:        /tmp/gapView.525877.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    1.3e-64  204.2   1.0    1.5e-64  204.0   1.0    1.0  1  NCBI__GCF_000733765.1:WP_043767302.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000733765.1:WP_043767302.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  204.0   1.0   1.5e-64   1.5e-64       1     227 [.       6     240 ..       6     241 .. 0.94

  Alignments for each domain:
  == domain 1  score: 204.0 bits;  conditional E-value: 1.5e-64
                             TIGR00419   1 lviinfKlnesvgkvelevaklaeevaseagvevavappfvdldvvkdeve.seiqvaAqnvd.avksGaftG 71 
                                           lv  n+K+++ +   e  +a+ +    + agv v++ pp  +l  v+  ++ s   ++Aq++  +v+sGa+tG
  NCBI__GCF_000733765.1:WP_043767302.1   6 LVAANWKMHGDRAFGE-ALARETVASCDDAGVDVVICPPICYLTLVAGPLSgSGCALGAQDLSpVVESGAHTG 77 
                                           6899***999876554.44544444457899********************99********975899****** PP

                             TIGR00419  72 eisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleere.......aartinn 137
                                           +i+ +ml d+Ga +v++gHsErR+   e +e +++k+  +++ gl++++Cvgetl+er+          ++++
  NCBI__GCF_000733765.1:WP_043767302.1  78 DINGAMLIDCGASHVIVGHSERRATRGEDNEAVAAKFLAAQQAGLTPILCVGETLAERDgerteavLEAQLDA 150
                                           **********************************************************999999887899*** PP

                             TIGR00419 138 vattaaaaAlepdvvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvlyGasvtaaedaela 210
                                           v   a++aA++ +v+A+EPv++iGtG+++s+ +a++ ++ +r  l++ ++ +a+svr++yG+sv+  ++a l+
  NCBI__GCF_000733765.1:WP_043767302.1 151 VVAAAGIAAFSRAVIAYEPVWAIGTGRTASPDQAQAAHAALRATLARDDARIADSVRIVYGGSVKPDNAASLF 223
                                           ************************************************************************* PP

                             TIGR00419 211 aqldvdGvLlasavlka 227
                                           aq+dvdG L+++a+lka
  NCBI__GCF_000733765.1:WP_043767302.1 224 AQPDVDGGLIGGASLKA 240
                                           ****************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (228 nodes)
Target sequences:                          1  (254 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 17.04
//
[ok]

This GapMind analysis is from Sep 24 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:

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:

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:

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:

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