GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tpi in Shewanella sp. ANA-3

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate 7023804 Shewana3_1026 triosephosphate isomerase (RefSeq)

Query= BRENDA::P0A858
         (255 letters)



>FitnessBrowser__ANA3:7023804
          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 7023804 Shewana3_1026 (triosephosphate isomerase (RefSeq))
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.3434398.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__ANA3:7023804  Shewana3_1026 triosephosphate is


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__ANA3:7023804  Shewana3_1026 triosephosphate isomerase (RefSeq)
   #    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........iqvaAqnvdavksGaf 69 
                                       +v +n+K+n+s    +++  k a ++ + +  ev++ pp ++l+ v++ +e++        ++++Aqn+  +++Ga+
  lcl|FitnessBrowser__ANA3:7023804   7 MVAGNWKMNGSAALAQELFKKFASKLQN-DSAEVVLCPPSIYLESVRQLLEANkealdgslVRMGAQNLSQHDFGAY 82 
                                       699**********************976.66899*********99976544221233333399************** PP

                         TIGR00419  70 tGeisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleere.......aartinnva 139
                                       tGe+s +mlkd+G+++v+igHsErR +  e+++++++k+a +++ gl++++Cvge+   re        a++++ v 
  lcl|FitnessBrowser__ANA3:7023804  83 TGEVSGQMLKDCGCRYVIIGHSERRRMYGETSNIVAEKFAAAQKHGLTPILCVGESGPAREarrtfevIAEELDIVI 159
                                       ********************************************************999997777877788888899 PP

                         TIGR00419 140 ttaaaaAlepdvvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvlyGasvtaaedaelaaqldvd 216
                                       ++++++A++++++A+EP +++GtGk++++ +a++v++++r  l++vs+ + e++r+lyG+svt +++a+l+aq+dvd
  lcl|FitnessBrowser__ANA3:7023804 160 QKNGTMAFDNAIIAYEPLWAVGTGKSATPEQAQEVHAFIRKRLSEVSPFIGENIRILYGGSVTPSNAADLFAQPDVD 236
                                       999999*********************************************************************** PP

                         TIGR00419 217 GvLlasavlk 226
                                       G L+++a+l 
  lcl|FitnessBrowser__ANA3:7023804 237 GGLIGGASLN 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 15.37
//
[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:

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