GapMind for catabolism of small carbon sources

 

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

Align Spermidine/putrescine import ATP-binding protein PotA, component of The spermidine/putrescine uptake porter, PotABCD (characterized)
to candidate 350222 BT0694 ABC transporter, ATP-binding protein (NCBI ptt file)

Query= TCDB::Q97Q42
         (385 letters)



>FitnessBrowser__Btheta:350222
          Length = 224

 Score =  136 bits (343), Expect = 5e-37
 Identities = 84/225 (37%), Positives = 125/225 (55%), Gaps = 10/225 (4%)

Query: 5   IIEFKNVSKVFEDSN--TKVLKDINFELEEGKFYTLLGASGSGKSTILNIIAGLLDATTG 62
           +I+ +N+SKVF  +   T  L  +N E++EG+F  ++G SG GKST+LNI+  L + T G
Sbjct: 1   MIQIENISKVFRTTEVETVALNHVNLEVKEGEFVAIMGPSGCGKSTLLNILGLLDNPTEG 60

Query: 63  DIMLDGVRINDIPTNKRD------VHTVFQSYALFPHMNVFENVAFPLRLRKIDKKEIEQ 116
              L G  +  +   +R       +  VFQS+ L   +NVFENV  PL    I   E  +
Sbjct: 61  SYRLLGEEVAGLKEKERTGVRKGKLGFVFQSFNLIDELNVFENVELPLTYLGIKSSERRR 120

Query: 117 RVAEVLKMVQLEGYEKRSIRKLSGGQRQRVAIARAIINQPRVVLLDEPLSALDLKLRTDM 176
            V ++LK + +    K   ++LSGGQ+QRVAIARA++  P+++L DEP   LD K   ++
Sbjct: 121 MVEDILKRMNISHRAKHFPQQLSGGQQQRVAIARAVVTNPKLILADEPTGNLDSKNGAEV 180

Query: 177 QYELRELQQRLGITFVFVTHDQEEALAMSDWIFVMNDGEIVQSGT 221
              L EL +  G T + VTH Q +A      + +  DG +V S T
Sbjct: 181 MNLLTELNKE-GTTIIMVTHSQHDASFAHRTVHLF-DGSVVASVT 223


Lambda     K      H
   0.318    0.138    0.386 

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: 225
Number of extensions: 13
Number of successful extensions: 2
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: 385
Length of database: 224
Length adjustment: 26
Effective length of query: 359
Effective length of database: 198
Effective search space:    71082
Effective search space used:    71082
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 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