GapMind for catabolism of small carbon sources

 

Alignments for a candidate for manA in Bacteroides clarus YIT 12056

Align Mannose-6-phosphate isomerase ManA; Phosphohexomutase; Phosphomannose isomerase; PMI; EC 5.3.1.8 (characterized)
to candidate WP_009120604.1 BUB52_RS12575 mannose-6-phosphate isomerase

Query= SwissProt::O31646
         (315 letters)



>NCBI__GCF_900129655.1:WP_009120604.1
          Length = 324

 Score =  187 bits (474), Expect = 4e-52
 Identities = 106/309 (34%), Positives = 170/309 (55%), Gaps = 16/309 (5%)

Query: 5   PLFFKPVFKERIWGGTALADFGY---TIPSQRTGECWAFAAHQNGQSVVQNGMYKGFTLS 61
           PL F+P+ K+ +WGG  +  F +   T+P+   GE W  +A +  +SVV NG  KG+TL 
Sbjct: 3   PLKFEPILKQTLWGGDKIIPFKHLDETLPN--VGESWEVSAVEGSESVVANGADKGYTLP 60

Query: 62  ELWEHHR-HLFGQLE----GDRFPLLTKILDADQDLSVQVHPNDEYANIHENGELGKTEC 116
           E+   ++  L G+      G++FPLL K +DA  DLS+QVHP DE A    N   GK E 
Sbjct: 61  EMVRKYKDELVGEANYARFGNKFPLLIKFIDAKLDLSIQVHPGDELAKKRHNS-FGKNEM 119

Query: 117 WYIIDCQKDAEIIYGHNAT-TKEELTTMIERGEWDELLRRVKVKPGDFFYVPSGTVHAIG 175
           WY+I   K A++I G +   T +E    +  G + E+L+   ++PGD FYVP+G VH IG
Sbjct: 120 WYVIAADKGAKLISGFSEEITPKEYKDRVHNGTFAEVLQTCTIEPGDAFYVPAGRVHGIG 179

Query: 176 KGILALETQQNSDTTYRLYDYDRKDAEGKLRELHLKKSIEVIEVPSIPERHTVHHEQIED 235
            G    E QQ SD TYR++DY+RKD +GK R+LH  ++++ I    + +     +E+I +
Sbjct: 180 AGAFVAEIQQTSDITYRIFDYNRKDKDGKSRDLHTSQAMDAINFSDVQDDFRTEYERIRN 239

Query: 236 LLTTTLIECAYFSVGKWNLSG--SASLKQQKPFLLISVIEGEGRMI-SGEYVYPFKKGDH 292
                ++   YF+   ++++   +    +   F++   +EG  R+    +     + G+ 
Sbjct: 240 -EPVEMVASPYFTTSVYDMTEEITCDYSELDSFVIFICVEGSCRLTDDNQNEITLRAGET 298

Query: 293 MLLPYGLGE 301
           +LLP  + E
Sbjct: 299 VLLPAAVQE 307


Lambda     K      H
   0.319    0.138    0.425 

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: 315
Number of extensions: 17
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: 315
Length of database: 324
Length adjustment: 28
Effective length of query: 287
Effective length of database: 296
Effective search space:    84952
Effective search space used:    84952
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 (21.7 bits)
S2: 48 (23.1 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