Aligments for a candidate for livF in Bacteroides thetaiotaomicron VPI-5482

GapMind for catabolism of small carbon sources

Aligments for a candidate for livF in Bacteroides thetaiotaomicron VPI-5482

Align high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized)
to candidate 350090 BT0562 putative ABC transporter ATP-binding protein (NCBI ptt file)

Query= CharProtDB::CH_003736
         (237 letters)



>FitnessBrowser__Btheta:350090
          Length = 489

 Score =  109 bits (273), Expect = 9e-29
 Identities = 73/219 (33%), Positives = 121/219 (55%), Gaps = 10/219 (4%)

Query: 10  KVSAHYGKIQALHEVSLHINQGEIVTLIGANGAGKTTLLGTLCGDPRATSGRIVFDDKDI 69
           ++S  YGK++AL EVS  + QGE+  LIG +GAGK+TL   L     A  G    +  D+
Sbjct: 12  EISKSYGKVEALKEVSFAVEQGEVFGLIGPDGAGKSTLFRILTTLLLADKGTATVNGLDV 71

Query: 70  -TDWQTAKIMREAVAIVPEGRRVFSRMTVEENLAMGGFFAE--RDQFQERIKWVYELFPR 126
            TD+   K +R  V  +P    ++  ++VEENL    FFA       QE    + +++ +
Sbjct: 72  VTDY---KQIRTKVGYMPGRFSLYQDLSVEENLE---FFATVFHTLIQENYDLIKDIYQQ 125

Query: 127 LHERRIQRAGTMSGGEQQMLAIGRALMSNPRLLLLDEPSLGLAPIIIQQIFDTIEQLREQ 186
           +   + +RAG +SGG +Q LA+  +L+  P +L LDEP+ G+ P+  ++ +  +  LR+Q
Sbjct: 126 IEPFKKRRAGALSGGMKQKLALSCSLIHKPDILFLDEPTTGVDPVSRKEFWQMLRNLRKQ 185

Query: 187 GMTIFLVEQNANQALKLADRGYVLENGHVVLSDTGDALL 225
           G+TI +     ++A +  DR   + +G V   DT + +L
Sbjct: 186 GITIIVSTPIMDEA-RQCDRIAFINHGQVHGIDTPERIL 223



 Score = 82.8 bits (203), Expect = 1e-20
 Identities = 58/224 (25%), Positives = 116/224 (51%), Gaps = 10/224 (4%)

Query: 1   MEKVMLSFDKVSAHYGKIQALHEVSLHINQGEIVTLIGANGAGKTTLLGTLCGDPRATSG 60
           M   ++  ++++  +G   A+  +S  + +GEI   +GANGAGKTT +  LCG  R TSG
Sbjct: 243 MAAPVIEVEQLTKSFGHFTAVDHISFQVQRGEIFGFLGANGAGKTTAMRMLCGLSRPTSG 302

Query: 61  RIVFDDKDITDWQTAKIMREAVAIVPEGRRVFSRMTVEENLAM-GGFFAERD-QFQERIK 118
                  DI  ++ A+ ++  +  + +   ++  + V EN+ +  G +  ++ + +E+  
Sbjct: 303 VGKVAGYDI--FREAEQVKRHIGYMSQKFSLYEDLKVWENIRLFAGIYGMKEMEIEEKTD 360

Query: 119 WVYELFPRL--HERRIQRAGTMSGGEQQMLAIGRALMSNPRLLLLDEPSLGLAPIIIQQI 176
              EL  RL   + R      +  G +Q LA   ++   P+++ LDEP+ G+ P   +Q 
Sbjct: 361 ---ELLERLGFADERDTLVKNLPLGWKQKLAFSVSIFHEPKIVFLDEPTGGVDPATRRQF 417

Query: 177 FDTIEQLREQGMTIFLVEQNANQALKLADRGYVLENGHVVLSDT 220
           ++ I Q  ++G+T+F+     ++A +  +R  ++ +G +   DT
Sbjct: 418 WELIYQAADRGITVFVTTHYMDEA-EYCNRISIMVDGQIKALDT 460


Lambda     K      H
   0.321    0.137    0.390 

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: 251
Number of extensions: 15
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 237
Length of database: 489
Length adjustment: 28
Effective length of query: 209
Effective length of database: 461
Effective search space:    96349
Effective search space used:    96349
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: 49 (23.5 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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

GapMind for catabolism of small carbon sources