GapMind for catabolism of small carbon sources

 

Aligments for a candidate for tpi in Pedobacter sp. GW460-11-11-14-LB5

Align Triosephosphate isomerase; TIM; TPI; Triose-phosphate isomerase; EC 5.3.1.1 (characterized)
to candidate CA265_RS10795 CA265_RS10795 triose-phosphate isomerase

Query= SwissProt::Q8XKU1
         (248 letters)



>lcl|FitnessBrowser__Pedo557:CA265_RS10795 CA265_RS10795
           triose-phosphate isomerase
          Length = 253

 Score =  219 bits (559), Expect = 3e-62
 Identities = 110/249 (44%), Positives = 164/249 (65%), Gaps = 4/249 (1%)

Query: 1   MRTPIIAGNWKMHYTIDEAVKLVEELKPLVKDAKCE---VVVCPTFVCLDAVKKAVEGTN 57
           MR  I+AGNWKM+   +E V L  E+  +VKD +      ++C  F+ L+++ K + G +
Sbjct: 1   MRKKIVAGNWKMNLDYNEGVSLFSEIVNMVKDERKGDQLAIICSPFIHLNSLAK-LGGND 59

Query: 58  IKVGAQNMHFEEKGAFTGEIAPRMLEAMNIDYVIIGHSERREYFNETDETCNKKVKAAFA 117
           +K+GAQN+  +E GA+TGE + +M++++  +YVI+GHSERR+YF E+D    +K K A A
Sbjct: 60  VKIGAQNISDKESGAYTGETSAKMVKSVGAEYVILGHSERRQYFAESDALLAEKTKVALA 119

Query: 118 HNLTPILCCGETLEQRENGTTNDVIKAQITADLEGLTKEQAEKVVIAYEPIWAIGTGKTA 177
           + LTPI C GETL++R NG+  +V+K Q+   +  L +   +K+VIAYEP+WAIGTG TA
Sbjct: 120 NGLTPIFCIGETLDERNNGSYYEVLKKQLVEGIFSLAEADFKKLVIAYEPVWAIGTGLTA 179

Query: 178 TSDQANETIAAIRAMVAEMFGQEVADKVRIQYGGSVKPNTIAEQMAKSDIDGALVGGASL 237
           +  QA +  A IR+ +   +G  VAD   I YGGS  P+  A   +++DIDG L+GGASL
Sbjct: 180 SPVQAQDIHAFIRSEIQANYGFNVADDTTILYGGSCNPSNAASLFSQNDIDGGLIGGASL 239

Query: 238 VAADFAQIV 246
            + DF  I+
Sbjct: 240 KSRDFTDII 248


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: 174
Number of extensions: 6
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: 248
Length of database: 253
Length adjustment: 24
Effective length of query: 224
Effective length of database: 229
Effective search space:    51296
Effective search space used:    51296
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 CA265_RS10795 CA265_RS10795 (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.13177.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
    9.9e-63  198.0   0.0    1.2e-62  197.8   0.0    1.0  1  lcl|FitnessBrowser__Pedo557:CA265_RS10795  CA265_RS10795 triose-phosphate i


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Pedo557:CA265_RS10795  CA265_RS10795 triose-phosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  197.8   0.0   1.2e-62   1.2e-62       1     227 [.       5     241 ..       5     242 .. 0.89

  Alignments for each domain:
  == domain 1  score: 197.8 bits;  conditional E-value: 1.2e-62
                                  TIGR00419   1 lviinfKlnesvgkvelevaklaeevase.agveva.vappfvdldvvkdeveseiqvaAqnvdavks 66 
                                                +v +n+K+n   ++   + +++ + v +e +g ++a +  pf++l+ +++   ++++++Aqn+  ++s
  lcl|FitnessBrowser__Pedo557:CA265_RS10795   5 IVAGNWKMNLDYNEGVSLFSEIVNMVKDErKGDQLAiICSPFIHLNSLAKLGGNDVKIGAQNISDKES 72 
                                                6999***7777777777777777766654144555526889*******999999************** PP

                                  TIGR00419  67 GaftGeisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaart 134
                                                Ga+tGe+sA+m+k +Ga++v++gHsErR +++e+d l+++k  ++ + gl+++ C+getl+er+ ++ 
  lcl|FitnessBrowser__Pedo557:CA265_RS10795  73 GAYTGETSAKMVKSVGAEYVILGHSERRQYFAESDALLAEKTKVALANGLTPIFCIGETLDERNNGSY 140
                                                ******************************************************************99 PP

                                  TIGR00419 135 innvattaaaaA.......lepdvvAvEPveliGtGkpvskAeaevveksvrdhlkk.vskevaesvr 194
                                                 ++++++            +++ v+A+EPv++iGtG ++s+ +a+ +++++r  ++     +va+++ 
  lcl|FitnessBrowser__Pedo557:CA265_RS10795 141 YEVLKKQLVEGIfslaeadFKKLVIAYEPVWAIGTGLTASPVQAQDIHAFIRSEIQAnYGFNVADDTT 208
                                                9998887532222344667**********************************99987899******* PP

                                  TIGR00419 195 vlyGasvtaaedaelaaqldvdGvLlasavlka 227
                                                +lyG+s + +++a l+ q d+dG L+++a+lk+
  lcl|FitnessBrowser__Pedo557:CA265_RS10795 209 ILYGGSCNPSNAASLFSQNDIDGGLIGGASLKS 241
                                                *******************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (228 nodes)
Target sequences:                          1  (253 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 6.18
//
[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:

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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