GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tpi in Pontibacter ramchanderi LP43

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_101443424.1 BD749_RS06020 phosphoglycerate kinase

Query= BRENDA::P36204
         (654 letters)



>NCBI__GCF_002846395.1:WP_101443424.1
          Length = 399

 Score =  384 bits (986), Expect = e-111
 Identities = 197/395 (49%), Positives = 273/395 (69%), Gaps = 8/395 (2%)

Query: 5   TIRDVDLKGKRVIMRVDFNVPVK-DGVVQDDTRIRAALPTIKYALEQGAKVILLSHLGRP 63
           T+   +  GK+ ++RVDFNVP+  D  + DDTRIRAA+PTI+  L  G  VIL+SHLGRP
Sbjct: 3   TVDAYNFAGKKALVRVDFNVPLDADYRITDDTRIRAAVPTIQKILNDGGAVILMSHLGRP 62

Query: 64  KGEPSPEFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRFHPGE 123
           K  P  ++SL  +  RLS+     VKF    VG E  +  ++LK GE+LLLEN RFH  E
Sbjct: 63  KTGPEEKYSLRHLVDRLSKEFNTTVKFATDCVGPEAAQLAQDLKPGEILLLENLRFHKAE 122

Query: 124 TKNDPELAKFWASLADIHVNDAFGTAHRAHASNVGIAQFIPS--VAGFLMEKEIKFLSKV 181
            K D E A+  ++L D++VNDAFGTAHR HAS   IA++ P+  V G++M  E+    +V
Sbjct: 123 EKGDLEFARELSTLGDVYVNDAFGTAHREHASTAVIARYFPNDKVMGYVMHAELDNARRV 182

Query: 182 TYNPEKPYVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRVEED 241
             N E+PY  ++GGAK+SDKI +I  LM+K D +LIGG M +TF+KA G E+GSS VEED
Sbjct: 183 MDNAERPYTAIMGGAKISDKILIIEKLMDKVDNLLIGGGMSYTFVKADGGEIGSSLVEED 242

Query: 242 KIDLAKELLEKAKEKGVEIVLPVDAVIAQKI--EPGVEKKVVRIDDGIPEGWMGLDIGPE 299
           K++LA+ L+  A+EKGV +++PVD++IA +   E  V+     +   I   WMGLDIGP 
Sbjct: 243 KVELARRLIAMAREKGVNLMIPVDSIIADEFSNEANVD---TALSHHIKPLWMGLDIGPN 299

Query: 300 TIELFKQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGAITVVGGGDSAAA 359
             E++   + ++KT++WNGPMGVFE+ +F+ GT+ VA A+   T +GA +++GGGDSAAA
Sbjct: 300 AREMYADVIRNSKTILWNGPMGVFEMSNFSVGTEAVAEAVVDATRRGAYSLIGGGDSAAA 359

Query: 360 VNKFGLEDKFSHVSTGGGASLEFLEGKELPGIASI 394
           VN+ G  D+ S+VSTGGGA LE++EGK LPG+A+I
Sbjct: 360 VNQLGYADRVSYVSTGGGALLEYMEGKTLPGVAAI 394


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: 634
Number of extensions: 28
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 654
Length of database: 399
Length adjustment: 34
Effective length of query: 620
Effective length of database: 365
Effective search space:   226300
Effective search space used:   226300
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 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