Alignments for a candidate for tpi in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for tpi in Cupriavidus basilensis 4G11

Align Triosephosphate isomerase; TIM; TPI; Triose-phosphate isomerase; EC 5.3.1.1 (characterized)
to candidate RR42_RS05495 RR42_RS05495 triosephosphate isomerase

Query= SwissProt::Q5SJR1
         (250 letters)



>FitnessBrowser__Cup4G11:RR42_RS05495
          Length = 245

 Score =  228 bits (582), Expect = 7e-65
 Identities = 124/245 (50%), Positives = 159/245 (64%), Gaps = 3/245 (1%)

Query: 1   MRRVLVAGNWKMHKTPSEARVWFAELKRLLPPLQSEAAVLPAFPILPVAKEVLAETQVGY 60
           MR+ LV GNWKMH + +        +K    P  +  AV   FP L   + +LA + V +
Sbjct: 1   MRQKLVIGNWKMHGSLAANVTLLEAIKAA--PASARLAVCAPFPYLAQCQALLAGSAVAW 58

Query: 61  GAQDVSAHKEGAYTGEVSARMLSDLGCRYAIVGHSERRRYHGETDALVAEKAKRLLEEGI 120
           GAQDVSA   GA+TGEV+A ML++ G  YA+VGHSERR YHGETDA VA KA R LE GI
Sbjct: 59  GAQDVSAEARGAFTGEVAASMLAEFGASYALVGHSERRSYHGETDATVAAKAVRALEFGI 118

Query: 121 TPILCVGEPLEVREKGEAVPYTLRQLRGSLEGVEPPGPEALVIAYEPVWAIGTGKNATPE 180
            P++CVGE L  RE GE      RQL   LE +       +V+AYEPVWAIGTGK A+ E
Sbjct: 119 VPVVCVGESLAQREAGETEAVVGRQLGAVLEALSLDQLGRIVLAYEPVWAIGTGKTASSE 178

Query: 181 DAEAMHQAIRKALSERYGEAFASRVRILYGGSVNPKNFADLLSMPNVDGGLVGGASLELE 240
            A+A+H  +R  ++ R     A+R+ +LYGGSV P N A+L SMP++DGGL+GGASL+ +
Sbjct: 179 QAQAVHAFLRAQVAAR-DAGVAARMAMLYGGSVKPDNAAELFSMPDIDGGLIGGASLKSD 237

Query: 241 SFLAL 245
            FLA+
Sbjct: 238 DFLAI 242


Lambda     K      H
   0.317    0.135    0.393 

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: 185
Number of extensions: 7
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: 250
Length of database: 245
Length adjustment: 24
Effective length of query: 226
Effective length of database: 221
Effective search space:    49946
Effective search space used:    49946
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 RR42_RS05495 RR42_RS05495 (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.12122.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    6.7e-62  195.3   1.2    7.6e-62  195.1   1.2    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS05495  RR42_RS05495 triosephosphate iso


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS05495  RR42_RS05495 triosephosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  195.1   1.2   7.6e-62   7.6e-62       1     228 []       5     237 ..       5     237 .. 0.93

  Alignments for each domain:
  == domain 1  score: 195.1 bits;  conditional E-value: 7.6e-62
                                 TIGR00419   1 lviinfKlnesvgkvelevaklaeevaseagvevavappfvdldvvkdeve.seiqvaAqnvdavksGa 68 
                                               lvi+n+K+++s+    +++  +++    +a   +av  pf +l   +  +  s +  +Aq+v a   Ga
  lcl|FitnessBrowser__Cup4G11:RR42_RS05495   5 LVIGNWKMHGSLAANVTLLEAIKA---APASARLAVCAPFPYLAQCQALLAgSAVAWGAQDVSAEARGA 70 
                                               79**********999999999985...6777899**************99999**************** PP

                                 TIGR00419  69 ftGeisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartinn 137
                                               ftGe+ A ml+++Ga + l+gHsErRs++ e+d  +++k  r+ e g+ +vvCvge+l++rea++t  +
  lcl|FitnessBrowser__Cup4G11:RR42_RS05495  71 FTGEVAASMLAEFGASYALVGHSERRSYHGETDATVAAKAVRALEFGIVPVVCVGESLAQREAGETEAV 139
                                               **************************************************************6666666 PP

                                 TIGR00419 138 vattaaaaA.......lepdvvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvlyGa 199
                                               v ++ +a+        l   v+A+EPv++iGtGk++s  +a++v++++r  ++  ++ va  + +lyG+
  lcl|FitnessBrowser__Cup4G11:RR42_RS05495 140 VGRQLGAVLealsldqLGRIVLAYEPVWAIGTGKTASSEQAQAVHAFLRAQVAARDAGVAARMAMLYGG 208
                                               666666654556666699*************************************************** PP

                                 TIGR00419 200 svtaaedaelaaqldvdGvLlasavlkae 228
                                               sv+  ++ael+  +d+dG L+++a+lk++
  lcl|FitnessBrowser__Cup4G11:RR42_RS05495 209 SVKPDNAAELFSMPDIDGGLIGGASLKSD 237
                                               ***************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (228 nodes)
Target sequences:                          1  (245 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: 9.07
//
[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