GapMind for catabolism of small carbon sources

 

Alignments for a candidate for potA in Pseudomonas litoralis 2SM5

Align PotG aka B0855, component of Putrescine porter (characterized)
to candidate WP_090274680.1 BLU11_RS14815 polyamine ABC transporter ATP-binding protein

Query= TCDB::P31134
         (377 letters)



>NCBI__GCF_900105005.1:WP_090274680.1
          Length = 378

 Score =  424 bits (1090), Expect = e-123
 Identities = 221/368 (60%), Positives = 276/368 (75%), Gaps = 2/368 (0%)

Query: 9   QAKTRKALTPLLEIRNLTKSYDGQHAVDDVSLTIYKGEIFALLGASGCGKSTLLRMLAGF 68
           QA  +      ++I  ++K +D   AVDDV+LTI +GEIFALLG SG GKSTLLR+LAGF
Sbjct: 10  QAMAKAEPVEFVKIERVSKQFDDALAVDDVTLTINRGEIFALLGGSGSGKSTLLRILAGF 69

Query: 69  EQPSAGQIMLDGVDLSQVPPYLRPINMMFQSYALFPHMTVEQNIAFGLKQDKLPKAEIAS 128
           E PS G+++LDG +++ +PP+ RPINMMFQSYALFPHMTVEQNIAFGLKQDKL   EI+ 
Sbjct: 70  ETPSEGRVLLDGQNITALPPHKRPINMMFQSYALFPHMTVEQNIAFGLKQDKLSNTEISE 129

Query: 129 RVNEMLGLVHMQEFAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRDRM 188
           RV EML LVHM ++AKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLR +M
Sbjct: 130 RVAEMLKLVHMAKYAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRSQM 189

Query: 189 QLEVVDILERVGVTCVMVTHDQEEAMTMAGRIAIMNRGKFVQIGEPEEIYEHPTTRYSAE 248
           QLE+V+I+ERVGVTC+MVTHDQEEAMTMA RIAIM++G  VQ+G P +IYE P  R+ AE
Sbjct: 190 QLELVEIIERVGVTCIMVTHDQEEAMTMAQRIAIMDQGWIVQVGTPMDIYESPVNRHVAE 249

Query: 249 FIGSVNVFEGVLKERQEDGLVLDSPGLVHPLKVDADASV-VDNVPVHVALRPEKIMLCEE 307
           F+GSVN+FEG +    +D ++++ P L   + +    +   ++     ALRPEK+ +  E
Sbjct: 250 FVGSVNIFEGEIVADMDDHVIIECPQLDRQIYLGHGVTTRAEDKSAIYALRPEKVFVTTE 309

Query: 308 PPANGCNFAVGEVIHIAYLGDLSVYHVRLKSGQMISAQLQNAHRHRKGLPTWGDEVRLCW 367
            P    N+A GEV  IAYLG  SVY+++L SG+M+ A   N+ R R   PTW D+V + W
Sbjct: 310 QPEQPYNWAHGEVHDIAYLGGHSVYYIKLDSGKMVQAFFANSER-RLPRPTWEDKVYVSW 368

Query: 368 EVDSCVVL 375
           + D  VVL
Sbjct: 369 DDDGGVVL 376


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: 455
Number of extensions: 10
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: 377
Length of database: 378
Length adjustment: 30
Effective length of query: 347
Effective length of database: 348
Effective search space:   120756
Effective search space used:   120756
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 Sep 24 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