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.13749.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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 6.62
//
[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