GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SM_b21106 in Alkalihalobacterium alkalinitrilicum DSM 22532

Align ABC transporter for L-Fucose, ATPase component (characterized)
to candidate WP_078429421.1 BK574_RS17060 ABC transporter ATP-binding protein

Query= reanno::Smeli:SM_b21106
         (365 letters)



>NCBI__GCF_002019605.1:WP_078429421.1
          Length = 351

 Score =  199 bits (507), Expect = 7e-56
 Identities = 118/305 (38%), Positives = 173/305 (56%), Gaps = 12/305 (3%)

Query: 1   MAPVTLKKLVKRYG--ALEVVHGIDLEVKDREFIALVGPSGCGKSTTLRMIAGLEEVSGG 58
           M+ +    + K Y   A   V  ++LE+ + E I L+GPSGCGK+TTLRM+AG E+ + G
Sbjct: 1   MSFIQFDNVTKYYNRAATPAVDQLNLEILEGEIITLLGPSGCGKTTTLRMLAGFEQPTTG 60

Query: 59  AIEIGGRKVND----LPPRARNISMVFQSYALYPHMTVAENMGFSLKIAGRPAEEIKTRV 114
            I IG   V D    LPP  R I MVFQ YAL+PH+T+ +N+ F L        + K R 
Sbjct: 61  KIRIGDEVVYDDRRALPPEKRGIGMVFQDYALFPHLTIEKNVTFGLNRWKN--RDKKKRA 118

Query: 115 AEAAAILDLAHLLERRPSQLSGGQRQRVAMGRAIVRQPDVFLFDEPLSNLDAKLRTQVRT 174
            E   ++ L     R PS+LSGGQ+QRVA+ RA+  +P V L DEP SNLDA LR ++R 
Sbjct: 119 QEVLELVGLGEFGHRLPSELSGGQQQRVALARALAPRPKVILMDEPFSNLDAGLREKMRY 178

Query: 175 EIKKLHARMQATMIYVTHDQVEAMTLSDRIVIMRDGHIEQVGTPEDVFRRPATKFVAGFI 234
           ++  +  +  AT I VTHDQ +A  +SDR+V+M +G I+Q+  P++++R PA  FVA F+
Sbjct: 179 DVTNILRKANATAIIVTHDQKDAFAVSDRVVVMNEGIIQQIAAPKEMYRCPANCFVAQFV 238

Query: 235 GSPPMNMEEAVLTDGKLAFASGATLPLPPRFRSLVREGQKVTFGLRPDDVYPSGHGLHAG 294
           G   + +   +  D K        + LP     ++   + V   +RP+    +  G +AG
Sbjct: 239 GKTNL-ISGTLCPDLKHVETHIGRVCLPQETDKVI---ENVMVSIRPEGCRLAEKGRYAG 294

Query: 295 DADAV 299
             + V
Sbjct: 295 LVERV 299


Lambda     K      H
   0.320    0.137    0.397 

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: 287
Number of extensions: 13
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: 365
Length of database: 351
Length adjustment: 29
Effective length of query: 336
Effective length of database: 322
Effective search space:   108192
Effective search space used:   108192
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 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