GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braF in Shewanella loihica PV-4

Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate 5210167 Shew_2611 ABC transporter-related protein (RefSeq)

Query= uniprot:Q1MCU2
         (292 letters)



>FitnessBrowser__PV4:5210167
          Length = 265

 Score =  187 bits (476), Expect = 2e-52
 Identities = 111/272 (40%), Positives = 166/272 (61%), Gaps = 22/272 (8%)

Query: 12  DTLLKVEHLSMKFGGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGFYKPTMGMI 71
           DT+L V+ +S+ FGG+ A+ D SFE +RG + ++IGPNGAGKT++ N I+G Y+P  G I
Sbjct: 3   DTILTVDQISLAFGGVKALTDVSFEVERGAVFSIIGPNGAGKTSMLNSISGRYRPQKGTI 62

Query: 72  TFNQKSGKQYLLERLPDFRITKEARVARTFQNIRLFSGLTVLENLLVAQHNKLMKASGYT 131
            F+     Q +    P+ R   +  + RTFQN+ LF  ++VL+N++V +H+ LMK +  T
Sbjct: 63  HFDN----QDVTHLRPNARA--DLGIGRTFQNLALFGHMSVLDNIMVGRHH-LMKNNWLT 115

Query: 132 ILGLIGVGP-YKREAAEAIELARFWLEKADLIDRAD------DPAGDLPYGAQRRLEIAR 184
                  GP Y    A+  ELA    +  ++ID  D        AG L YG ++R+E+AR
Sbjct: 116 -------GPLYWASPAQKEELAHR-RQVEEIIDFLDISHVRKSIAGTLSYGLRKRVELAR 167

Query: 185 AMCTGPELLCLDEPAAGLNPRESATLNALLKSIRAETGTSILLIEHDMSVVMEISDHVVV 244
           AM   P+L+ LDEP AG+N  E   +   +  +  E G ++++IEHDM VVM+IS  V+V
Sbjct: 168 AMALNPKLILLDEPMAGMNLEEKEDMARYILDLNEEFGITVVMIEHDMGVVMDISHEVMV 227

Query: 245 LEYGQKISDGTPDHVKNDPRVIAAYLGVEDEE 276
           L++G+K+  G P+ V  D  V  AYLG+ED+E
Sbjct: 228 LDFGKKLISGLPEAVMADEHVRQAYLGLEDDE 259


Lambda     K      H
   0.318    0.136    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: 195
Number of extensions: 8
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: 292
Length of database: 265
Length adjustment: 25
Effective length of query: 267
Effective length of database: 240
Effective search space:    64080
Effective search space used:    64080
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: 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