GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galU in Malonomonas rubra DSM 5091

Align UTP-glucose-1-phosphate uridylyltransferase (EC 2.7.7.9) (characterized)
to candidate WP_072908932.1 BUB13_RS11620 mannose-1-phosphate guanyltransferase

Query= BRENDA::P74285
         (388 letters)



>NCBI__GCF_900142125.1:WP_072908932.1
          Length = 838

 Score =  187 bits (475), Expect = 1e-51
 Identities = 105/323 (32%), Positives = 177/323 (54%), Gaps = 16/323 (4%)

Query: 1   MKAMILAAGKGTRVRPITHTIPKPMIPILQKPVMEFLLELLRQHGFDQIMVNVSHLAEEI 60
           MKA+I+A G GTR+ P++  +PKPM+P+  +P+M  +++LL++HG  ++++ +    + +
Sbjct: 1   MKAVIMAGGFGTRLHPLSINLPKPMVPLCNRPIMLHIVDLLKKHGITELVMLLYFQPDTV 60

Query: 61  ESYFRDGQRFGVQIAYSFEGNIVDGDLVGKALGSAGGLKKIQEFNPFFDDTFVVLCGDAL 120
           + +F DG  +GV I Y             + LG+AG +K         D+ F+++ GD L
Sbjct: 61  KKFFGDGSEYGVNITYVTPL---------EDLGTAGAVKAAARH---LDERFLIISGDLL 108

Query: 121 IDLDLTTAVKLHREKGAIATIITKTVPQELVSSYGVVVTDDNGKILTFQEKPAVEEALST 180
            D DLT A+K H  K A AT+   +VP  L   +GVV+T+  G+I  F EKP   E  S 
Sbjct: 109 TDFDLTAAIKFHEAKNAKATLTLTSVPDPL--QFGVVITNQKGEITKFLEKPDWGEVFSD 166

Query: 181 EINTGIYIFEPEVIDYIPSGQEYDLGGDLFPKLVDSGLPFYAVNMDFEWVDIGKVPDYWQ 240
            INTGIYI EPEV+D IP G+  D   D+FP+L+      Y   +   W DIG    Y +
Sbjct: 167 TINTGIYILEPEVLDLIPEGENRDWSKDIFPQLLQQKDRLYGCTLKGYWQDIGNTDAYLE 226

Query: 241 AIRGVLSREIKNVQIPGIEVRPGVYTGINVAANWDNIE-IEGPVYIGGMTRIEDGVKIIG 299
             + +++ +++      +  +  V+ G   + + D  + + G V +G  TR+    K+  
Sbjct: 227 TCKDIMAGKVEIEIDETLTEKKKVFFGAETSVSEDTQKALRGMVVLGDNTRLVGKPKLKN 286

Query: 300 PSMIGPSCLICQGAVVDNSVIFE 322
             +IG +C I  GA +++ ++++
Sbjct: 287 -CLIGRNCTIEDGAELEDCILWD 308


Lambda     K      H
   0.321    0.141    0.418 

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: 717
Number of extensions: 28
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: 388
Length of database: 838
Length adjustment: 36
Effective length of query: 352
Effective length of database: 802
Effective search space:   282304
Effective search space used:   282304
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Apr 09 2024. 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