GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS17020 in Alkalihalobacterium alkalinitrilicum DSM 22532

Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate WP_078429421.1 BK574_RS17060 ABC transporter ATP-binding protein

Query= uniprot:D8IPI1
         (406 letters)



>NCBI__GCF_002019605.1:WP_078429421.1
          Length = 351

 Score =  210 bits (534), Expect = 6e-59
 Identities = 122/296 (41%), Positives = 174/296 (58%), Gaps = 14/296 (4%)

Query: 1   MADIHCQALAKHY-AGGPPVLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGG 59
           M+ I    + K+Y     P +  L+L I +GE + LLGPSGCGK+T LRM+AG E  + G
Sbjct: 1   MSFIQFDNVTKYYNRAATPAVDQLNLEILEGEIITLLGPSGCGKTTTLRMLAGFEQPTTG 60

Query: 60  TLRIGGTVVND----LPARERNVAMVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRV 115
            +RIG  VV D    LP  +R + MVFQ+YAL+PH+++  N+ FGL R K    +  +R 
Sbjct: 61  KIRIGDEVVYDDRRALPPEKRGIGMVFQDYALFPHLTIEKNVTFGLNRWKN--RDKKKRA 118

Query: 116 REVAALLNLEALLERKPRAMSGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRG 175
           +EV  L+ L     R P  +SGGQQQR A+ARA+   P V L DEP SNLDA LR ++R 
Sbjct: 119 QEVLELVGLGEFGHRLPSELSGGQQQRVALARALAPRPKVILMDEPFSNLDAGLREKMRY 178

Query: 176 DIKRLHQRLRTTTVYVTHDQLEAMTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFI 235
           D+  + ++   T + VTHDQ +A  ++DRV++M +G I Q  +P E+YR P N F A F+
Sbjct: 179 DVTNILRKANATAIIVTHDQKDAFAVSDRVVVMNEGIIQQIAAPKEMYRCPANCFVAQFV 238

Query: 236 GTPAMNFLSGTVQRQDGQLFIETAHQRWALTGERFSRLRHAMAVKLAVRPDHVRIA 291
           G    N +SGT+        +ET   R  L  E    + + M   +++RP+  R+A
Sbjct: 239 G--KTNLISGTL--CPDLKHVETHIGRVCLPQETDKVIENVM---VSIRPEGCRLA 287


Lambda     K      H
   0.321    0.137    0.403 

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: 301
Number of extensions: 15
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: 406
Length of database: 351
Length adjustment: 30
Effective length of query: 376
Effective length of database: 321
Effective search space:   120696
Effective search space used:   120696
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: 50 (23.9 bits)

This GapMind analysis is from Apr 09 2024. 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