GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Pedo557:CA265_RS01880
          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:

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