GapMind for catabolism of small carbon sources

 

Alignments for a candidate for manA in Bacteroides thetaiotaomicron VPI-5482

Align Mannose-6-phosphate isomerase ManA; Phosphohexomutase; Phosphomannose isomerase; PMI; EC 5.3.1.8 (characterized)
to candidate 349901 BT0373 mannose-6-phosphate isomerase (NCBI ptt file)

Query= SwissProt::O31646
         (315 letters)



>FitnessBrowser__Btheta:349901
          Length = 323

 Score =  181 bits (459), Expect = 2e-50
 Identities = 106/302 (35%), Positives = 167/302 (55%), Gaps = 13/302 (4%)

Query: 5   PLFFKPVFKERIWGGTALADFGYTIPSQR-TGECWAFAAHQNGQSVVQNGMYKGFTLSEL 63
           PL F+P+ K+ +WGG  +  F +     +  GE W  +  ++ +SVV NG  KG TL+++
Sbjct: 3   PLKFEPILKQTLWGGDKIIPFKHLNSDLKGVGESWEISGVEDNESVVANGPDKGLTLADM 62

Query: 64  WEHHRH-LFGQLE----GDRFPLLTKILDADQDLSVQVHPNDEYANIHENGELGKTECWY 118
              +R  L G+      G++FPLL K +DA QDLS+QVHP D+ A    N  +GKTE WY
Sbjct: 63  VRKYREELVGEANYARFGNKFPLLIKFIDAKQDLSIQVHPADDLAKKRHNS-MGKTEMWY 121

Query: 119 IIDCQKDAEIIYGHNAT-TKEELTTMIERGEWDELLRRVKVKPGDFFYVPSGTVHAIGKG 177
           ++D  K A++  G +   T +E    +      ++L+  ++KPGD F++P+G VH+IG G
Sbjct: 122 VVDADKGAKLRSGFSEQITPKEYKERVLNNTITDVLQEYEIKPGDVFFLPAGRVHSIGAG 181

Query: 178 ILALETQQNSDTTYRLYDYDRKDAEGKLRELHLKKSIEVIEVPSIPERHTVHHEQIEDLL 237
               E QQ SD TYR+YD++RKDA GK RELH   + E I    + +  T  +E ++D  
Sbjct: 182 AFIAEIQQTSDITYRIYDFNRKDANGKTRELHTDLAREAINYEVLDDYRT-KYEAVKD-E 239

Query: 238 TTTLIECAYFSVGKWNLSG--SASLKQQKPFLLISVIEGEGRMISGE-YVYPFKKGDHML 294
              L+ C YF+   ++++   S    +   F++   +EG  ++   E        G+ +L
Sbjct: 240 PVELVACPYFTTSVYDMTEEISCDYSELDSFVIFICMEGACKIKDNEGNELKVGAGESIL 299

Query: 295 LP 296
           LP
Sbjct: 300 LP 301


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: 293
Number of extensions: 18
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: 323
Length adjustment: 28
Effective length of query: 287
Effective length of database: 295
Effective search space:    84665
Effective search space used:    84665
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 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