GapMind for catabolism of small carbon sources

 

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

Align PP1068, component of Acidic amino acid uptake porter, AatJMQP (characterized)
to candidate 350849 BT1321 putative phosphate transport ATP-binding protein (NCBI ptt file)

Query= TCDB::Q88NY5
         (256 letters)



>FitnessBrowser__Btheta:350849
          Length = 252

 Score =  136 bits (343), Expect = 4e-37
 Identities = 92/247 (37%), Positives = 132/247 (53%), Gaps = 16/247 (6%)

Query: 10  DLRMISIKNVNKWYGDFQVLTDCSTEVKKGEVVVVCGPSGSGKSTLIKCVNALEPF---- 65
           D   I  ++VN WYGDF  L   S ++++  VV   GPSG GKST ++  N +       
Sbjct: 2   DTVKIDTRDVNFWYGDFHALKGISMQIEEKSVVAFIGPSGCGKSTFLRLFNRMNDLIPAT 61

Query: 66  -QKGDIVVDGTSIADPKTNLPKLRSRVGMVFQHFELFPHLTITENLTIAQR------KVL 118
             +G+I +DG +I      + +LR  VGMVFQ    FP  +I EN+    R         
Sbjct: 62  RLEGEIRIDGHNIYAKGVEVDELRKNVGMVFQRPNPFPK-SIFENVAYGLRVNGVKDNAF 120

Query: 119 GRSEAEATKKGLALLDRVGLSAHAKKHPGQLSGGQQQRVAIARALAMDPIVMLFDEPTSA 178
            R   E T KG AL D V      K+    LSGGQQQR+ IARA+A+ P V+L DEP SA
Sbjct: 121 IRQRVEETLKGAALWDEV--KDKLKESAYALSGGQQQRLCIARAMAVSPSVLLMDEPASA 178

Query: 179 LDPEMVSEVLDVMVQLAQEGMTMMCVTHEMGFARKVANRVIFMDKGSIIE-DCTKEEFFG 237
           LDP   ++V +++ +L ++  T++ VTH M  A +V+++  F   G ++E D TK+ F  
Sbjct: 179 LDPISTAKVEELIHELKKD-YTIVIVTHNMQQAARVSDKTAFFYLGEMVEYDDTKKIFTN 237

Query: 238 DQSARDQ 244
            +    Q
Sbjct: 238 PEKEATQ 244


Lambda     K      H
   0.319    0.134    0.383 

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: 112
Number of extensions: 4
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: 256
Length of database: 252
Length adjustment: 24
Effective length of query: 232
Effective length of database: 228
Effective search space:    52896
Effective search space used:    52896
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: 47 (22.7 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