GapMind for catabolism of small carbon sources

 

Alignments for a candidate for potA in Alkalihalobacterium alkalinitrilicum DSM 22532

Align PotG aka B0855, component of Putrescine porter (characterized)
to candidate WP_078429421.1 BK574_RS17060 ABC transporter ATP-binding protein

Query= TCDB::P31134
         (377 letters)



>NCBI__GCF_002019605.1:WP_078429421.1
          Length = 351

 Score =  234 bits (596), Expect = 4e-66
 Identities = 141/338 (41%), Positives = 198/338 (58%), Gaps = 40/338 (11%)

Query: 20  LEIRNLTKSYD--GQHAVDDVSLTIYKGEIFALLGASGCGKSTLLRMLAGFEQPSAGQIM 77
           ++  N+TK Y+     AVD ++L I +GEI  LLG SGCGK+T LRMLAGFEQP+ G+I 
Sbjct: 4   IQFDNVTKYYNRAATPAVDQLNLEILEGEIITLLGPSGCGKTTTLRMLAGFEQPTTGKIR 63

Query: 78  L-DGV---DLSQVPPYLRPINMMFQSYALFPHMTVEQNIAFGLKQDKLPKAEIASRVNEM 133
           + D V   D   +PP  R I M+FQ YALFPH+T+E+N+ FGL + K    +   R  E+
Sbjct: 64  IGDEVVYDDRRALPPEKRGIGMVFQDYALFPHLTIEKNVTFGLNRWK--NRDKKKRAQEV 121

Query: 134 LGLVHMQEFAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRDRMQLEVV 193
           L LV + EF  R P +LSGGQ+QRVALAR+LA RPK++L+DEP   LD  LR++M+ +V 
Sbjct: 122 LELVGLGEFGHRLPSELSGGQQQRVALARALAPRPKVILMDEPFSNLDAGLREKMRYDVT 181

Query: 194 DILERVGVTCVMVTHDQEEAMTMAGRIAIMNRGKFVQIGEPEEIYEHPTTRYSAEFIGSV 253
           +IL +   T ++VTHDQ++A  ++ R+ +MN G   QI  P+E+Y  P   + A+F+G  
Sbjct: 182 NILRKANATAIIVTHDQKDAFAVSDRVVVMNEGIIQQIAAPKEMYRCPANCFVAQFVGKT 241

Query: 254 NVFEGVLKERQEDGLVLDSPGLVH----------PLKVDADASVVDNVPVHVALRPEKIM 303
           N+  G L            P L H          P + D    V++N  V V++RPE   
Sbjct: 242 NLISGTL-----------CPDLKHVETHIGRVCLPQETD---KVIEN--VMVSIRPEGCR 285

Query: 304 LCEEPPANGCNFAVGEVIHIAYLGDLSVYHVRLKSGQM 341
           L E+          G V  + Y G+    HVRL+S Q+
Sbjct: 286 LAEK------GRYAGLVERVTYSGEYQEVHVRLQSDQV 317


Lambda     K      H
   0.321    0.137    0.400 

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: 329
Number of extensions: 17
Number of successful extensions: 4
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: 377
Length of database: 351
Length adjustment: 29
Effective length of query: 348
Effective length of database: 322
Effective search space:   112056
Effective search space used:   112056
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