GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tpi in Nocardiopsis baichengensis YIM 90130

Align Triosephosphate isomerase; TIM; TPI; Triose-phosphate isomerase; EC 5.3.1.1 (characterized)
to candidate WP_017541731.1 C892_RS0126430 triose-phosphate isomerase

Query= SwissProt::Q9Z520
         (258 letters)



>NCBI__GCF_000341205.1:WP_017541731.1
          Length = 260

 Score =  353 bits (907), Expect = e-102
 Identities = 179/253 (70%), Positives = 202/253 (79%), Gaps = 1/253 (0%)

Query: 4   RTPLMAGNWKMNLNHLEAIAHVQKLAFALADKDYDAVEVAVLAPFTDLRSVQTLVDGDKL 63
           R PL+AGNWKMN NHLEAIA VQKLAFAL   DYD  EV VL PFTDLRSVQTLVDGDKL
Sbjct: 6   RKPLIAGNWKMNNNHLEAIALVQKLAFALDAADYDRAEVVVLPPFTDLRSVQTLVDGDKL 65

Query: 64  KIKYGAQDISAHDGGAYTGEISGPMLAKLKCTYVAVGHSERRQYHAETDEIVNAKVKAAY 123
            I YGAQD+S H+ GAYTGE+SGPMLAKL C+YV  GHSERR+YHAE D +VNAKVKAA+
Sbjct: 66  SIAYGAQDLSRHEKGAYTGEVSGPMLAKLGCSYVLAGHSERREYHAEDDALVNAKVKAAF 125

Query: 124 KHGLTPILCVGEELDVREAGNHVEHTLAQVEGGLKDLAAEQAESVVIAYEPVWAIGTGKV 183
            H +TPILCVGE L+VR+AG+ V HT AQVE  +K L AEQ E +VIAYEPVWAIGTG+V
Sbjct: 126 AHDITPILCVGEGLEVRKAGDQVAHTSAQVEAAVKGLTAEQVERLVIAYEPVWAIGTGEV 185

Query: 184 CGADDAQEVC-AAIRGKLAELYSQELADKVRIQYGGSVKSGNVAEIMAKPDIDGALVGGA 242
              DDAQEVC AA+R  LA LY +  A K R+ YGGSVK  N+  IMAK DIDGALVGGA
Sbjct: 186 ATPDDAQEVCGAAVRATLAGLYDEATAAKTRVLYGGSVKPDNIGGIMAKADIDGALVGGA 245

Query: 243 SLDSDEFVKIVRF 255
           SL +D+F K+V+F
Sbjct: 246 SLKADDFAKLVKF 258


Lambda     K      H
   0.316    0.133    0.381 

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: 285
Number of extensions: 12
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: 258
Length of database: 260
Length adjustment: 24
Effective length of query: 234
Effective length of database: 236
Effective search space:    55224
Effective search space used:    55224
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 WP_017541731.1 C892_RS0126430 (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.2762108.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    2.5e-56  177.0   1.1    2.9e-56  176.8   1.1    1.0  1  NCBI__GCF_000341205.1:WP_017541731.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000341205.1:WP_017541731.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  176.8   1.1   2.9e-56   2.9e-56       1     228 []       9     250 ..       9     250 .. 0.92

  Alignments for each domain:
  == domain 1  score: 176.8 bits;  conditional E-value: 2.9e-56
                             TIGR00419   1 lviinfKlnesvgkvelevaklae..evaseagvevavappfvdldvvkdeve...seiqvaAqnvdavksGa 68 
                                           l+ +n+K+n+   +   +v+kla   + a+ +  ev+v ppf dl+ v+  v+     i  +Aq++  +++Ga
  NCBI__GCF_000341205.1:WP_017541731.1   9 LIAGNWKMNNNHLEAIALVQKLAFalDAADYDRAEVVVLPPFTDLRSVQTLVDgdkLSIAYGAQDLSRHEKGA 81 
                                           689*******************975689********************99887532358899*********** PP

                             TIGR00419  69 ftGeisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartinnvatt 141
                                           +tGe+s  ml+ lG+ +vl gHsErR +++e d l+++kv  + + ++++++Cvge le r+a+ ++     +
  NCBI__GCF_000341205.1:WP_017541731.1  82 YTGEVSGPMLAKLGCSYVLAGHSERREYHAEDDALVNAKVKAAFAHDITPILCVGEGLEVRKAGDQVAHTSAQ 154
                                           **************************************************************88888877777 PP

                             TIGR00419 142 aaaaA.......lepdvvAvEPveliGtGkpvskAeaevve.ksvrdhlkk.vskevaesvrvlyGasvtaae 205
                                            +aa         e  v+A+EPv++iGtG ++++ +a++v  + vr  l+   ++  a ++rvlyG+sv+  +
  NCBI__GCF_000341205.1:WP_017541731.1 155 VEAAVkgltaeqVERLVIAYEPVWAIGTGEVATPDDAQEVCgAAVRATLAGlYDEATAAKTRVLYGGSVKPDN 227
                                           7776677777779999**********************996268*****997888899*************** PP

                             TIGR00419 206 daelaaqldvdGvLlasavlkae 228
                                               +a+ d+dG+L+++a+lka+
  NCBI__GCF_000341205.1:WP_017541731.1 228 IGGIMAKADIDGALVGGASLKAD 250
                                           *********************97 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: 20.72
//
[ok]

This GapMind analysis is from Sep 24 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