Alignments for a candidate for tpi in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Alignments for a candidate for tpi in Sinorhizobium meliloti 1021

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate SMc01614 SMc01614 triosephosphate isomerase

Query= BRENDA::Q7X216
         (265 letters)



>FitnessBrowser__Smeli:SMc01614
          Length = 255

 Score =  203 bits (517), Expect = 3e-57
 Identities = 116/255 (45%), Positives = 158/255 (61%), Gaps = 8/255 (3%)

Query: 5   IWLGTSWKMNKPLSQAMAWCETLAARMPEGCHPAIQPFVIPSFTAIQPVSHFLQTHQLPL 64
           +W+GTSWKMNK L++AM + + LAA   +     IQ FVIP FTA + V   L+   + +
Sbjct: 6   LWVGTSWKMNKTLAEAMVFADGLAAA-DDARDQRIQRFVIPPFTAARQVKERLKATSVKV 64

Query: 65  LTGAQNMHEADQGAWTGEISAAMLAETGATLVELGHSERRAAFNESDAAINRKVHSALGH 124
             GAQNMH  D GAWTGEIS  ML++    +VELGHSERR  F E+D  +  K  +A+ H
Sbjct: 65  --GAQNMHWDDAGAWTGEISPVMLSDCDLDIVELGHSERREHFGETDRTVGLKTAAAVKH 122

Query: 125 GLRPLICIGDSAEEKRWQVSRESVVRQMKIALYGL-SHQQALRTLIAYEPVWAIGEHGTP 183
           GL PLICIG++  ++    +   + RQ++ A   L    +    L+AYEPVWAIG +G P
Sbjct: 123 GLVPLICIGETLAQREAGEADTVLKRQVEGAFAFLEGAARKAPVLLAYEPVWAIGVNGIP 182

Query: 184 ASPQEAGVIHQALRQALCERFGHETGTRIPLLYGGXVTLQNAVELLRQQEINGLFIGRAA 243
           A+   A   H+ + + + ER     G ++P+LYGG V  QN  EL+ Q  I+GLFIGR+A
Sbjct: 183 ATADYADARHRLIGE-VAER---ALGVKVPVLYGGSVNPQNCEELILQPHIDGLFIGRSA 238

Query: 244 WDAQGYCDIVQRVTQ 258
           WD  GY DI+QRV +
Sbjct: 239 WDVGGYLDILQRVAR 253


Lambda     K      H
   0.321    0.133    0.412 

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: 231
Number of extensions: 9
Number of successful extensions: 5
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: 265
Length of database: 255
Length adjustment: 24
Effective length of query: 241
Effective length of database: 231
Effective search space:    55671
Effective search space used:    55671
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 47 (22.7 bits)

Align candidate SMc01614 SMc01614 (triosephosphate 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.18098.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
    1.8e-43  135.0   0.0    2.3e-43  134.7   0.0    1.0  1  lcl|FitnessBrowser__Smeli:SMc01614  SMc01614 triosephosphate isomera


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMc01614  SMc01614 triosephosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.7   0.0   2.3e-43   2.3e-43       2     221 ..       8     235 ..       7     239 .. 0.91

  Alignments for each domain:
  == domain 1  score: 134.7 bits;  conditional E-value: 2.3e-43
                           TIGR00419   2 viinfKlnesvgkvelevaklae.evaseagvevavappfvdldvvkdeve.seiqvaAqnvdavksGaftGeis 74 
                                         v+  +K+n ++ +       la+ + a  + ++  v ppf   + vk++++ + ++v+Aqn++  ++Ga+tGeis
  lcl|FitnessBrowser__Smeli:SMc01614   8 VGTSWKMNKTLAEAMVFADGLAAaDDARDQRIQRFVIPPFTAARQVKERLKaTSVKVGAQNMHWDDAGAWTGEIS 82 
                                         6789**********9999999988999999*********************899********************* PP

                           TIGR00419  75 AemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartinnvatta..aaaA. 146
                                           ml d+    v +gHsErR ++ e+d  ++ k a + + gl +++C+getl++rea++  ++v++ +  +a A 
  lcl|FitnessBrowser__Smeli:SMc01614  83 PVMLSDCDLDIVELGHSERREHFGETDRTVGLKTAAAVKHGLVPLICIGETLAQREAGEA-DTVLKRQveGAFAf 156
                                         ********************************************************8876.45544441134446 PP

                           TIGR00419 147 ......lepdvvAvEPveliG.tGkpvskAeaevveksvrdhlkkvskevaesvrvlyGasvtaaedaelaaqld 214
                                                 p+++A+EPv++iG  G+p++   a++ +  +    + +++ +  +v vlyG+sv+ +++ el++q+ 
  lcl|FitnessBrowser__Smeli:SMc01614 157 legaarKAPVLLAYEPVWAIGvNGIPATADYADARHRLIG---EVAERALGVKVPVLYGGSVNPQNCEELILQPH 228
                                         6666667899***********56**************999...668899999*********************** PP

                           TIGR00419 215 vdGvLla 221
                                         +dG+ ++
  lcl|FitnessBrowser__Smeli:SMc01614 229 IDGLFIG 235
                                         ****998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (228 nodes)
Target sequences:                          1  (255 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: 6.84
//
[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