GapMind for catabolism of small carbon sources

 

Aligments for a candidate for tpi in Pedobacter sp. GW460-11-11-14-LB5

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate CA265_RS01880 CA265_RS01880 phosphoglycerate kinase

Query= BRENDA::P36204
         (654 letters)



>lcl|FitnessBrowser__Pedo557:CA265_RS01880 CA265_RS01880
           phosphoglycerate kinase
          Length = 397

 Score =  399 bits (1026), Expect = e-115
 Identities = 207/394 (52%), Positives = 275/394 (69%), Gaps = 5/394 (1%)

Query: 5   TIRDVDLKGKRVIMRVDFNVPVKDGV-VQDDTRIRAALPTIKYALEQGAKVILLSHLGRP 63
           TI   D K K+ ++RVDFNVP+ D   + DD RIRAALPTI   L+ G  VIL+SHLGRP
Sbjct: 3   TIDQFDFKDKKALIRVDFNVPLDDEFKITDDKRIRAALPTISKILKDGGAVILMSHLGRP 62

Query: 64  KGEPSPEFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRFHPGE 123
           K  P+ ++SL  +   LS L+G EVKF    +G+   K   +LK GEVLLLEN RF+  E
Sbjct: 63  KDGPTDKYSLKHILSDLSALVGVEVKFADDCIGESAVKQAADLKSGEVLLLENLRFYKEE 122

Query: 124 TKNDPELAKFWASLADIHVNDAFGTAHRAHASNVGIAQFIPSVA--GFLMEKEIKFLSKV 181
            K D   A+  + L D++VNDAFGTAHRAHAS   IAQF P     G+LM  E++   K+
Sbjct: 123 EKGDVAFAEKLSKLGDVYVNDAFGTAHRAHASTSIIAQFFPDAKYFGYLMASEVENAEKI 182

Query: 182 TYNPEKPYVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRVEED 241
             + E+P+  ++GGAKVSDKI +I  L++K D ++IGG M +TF KA G E+G+S +E D
Sbjct: 183 LNHAERPFTAIMGGAKVSDKILLIEKLLDKVDNLIIGGGMAYTFAKAQGGEIGTSLLEAD 242

Query: 242 KIDLAKELLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDGIPEGWMGLDIGPETI 301
           K +L+ EL+EKAK KGV ++LPVD VIA K     +KK V     IP  WMGLDIGP+++
Sbjct: 243 KQELSLELIEKAKAKGVNLILPVDTVIADKFANDADKKDV-TSGQIPADWMGLDIGPKSV 301

Query: 302 ELFKQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALT-EKGAITVVGGGDSAAAV 360
            LF+  + ++KT++WNGPMGVFE++ F  GTK VA A+ A T + GA +++GGGDSAAA+
Sbjct: 302 ALFQDVIKNSKTLLWNGPMGVFEMESFQVGTKAVAEAVVAATKDNGAFSLIGGGDSAAAI 361

Query: 361 NKFGLEDKFSHVSTGGGASLEFLEGKELPGIASI 394
            KFG+ED+ S+VSTGGGA LE++EGKELPG+ +I
Sbjct: 362 AKFGMEDEVSYVSTGGGALLEYMEGKELPGVKAI 395


Lambda     K      H
   0.317    0.137    0.386 

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: 710
Number of extensions: 38
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: 654
Length of database: 397
Length adjustment: 34
Effective length of query: 620
Effective length of database: 363
Effective search space:   225060
Effective search space used:   225060
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: 52 (24.6 bits)

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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