GapMind for catabolism of small carbon sources

 

Alignments for a candidate for potA in Klebsiella michiganensis M5al

Align PotG aka B0855, component of Putrescine porter (characterized)
to candidate BWI76_RS09465 BWI76_RS09465 polyamine ABC transporter ATP-binding protein

Query= TCDB::P31134
         (377 letters)



>FitnessBrowser__Koxy:BWI76_RS09465
          Length = 392

 Score =  700 bits (1806), Expect = 0.0
 Identities = 348/377 (92%), Positives = 364/377 (96%)

Query: 1   MNDAIPRPQAKTRKALTPLLEIRNLTKSYDGQHAVDDVSLTIYKGEIFALLGASGCGKST 60
           +ND IPRPQAKT KALTPLLEIRNLTKS+DGQHAVDDV+LTIYKGEIFALLGASGCGKST
Sbjct: 16  VNDVIPRPQAKTPKALTPLLEIRNLTKSFDGQHAVDDVNLTIYKGEIFALLGASGCGKST 75

Query: 61  LLRMLAGFEQPSAGQIMLDGVDLSQVPPYLRPINMMFQSYALFPHMTVEQNIAFGLKQDK 120
           LLRMLAGFEQP+AGQI+LDGVDL++VPPY RPINMMFQSYALFPHMTVEQNIAFGLKQDK
Sbjct: 76  LLRMLAGFEQPTAGQIVLDGVDLARVPPYQRPINMMFQSYALFPHMTVEQNIAFGLKQDK 135

Query: 121 LPKAEIASRVNEMLGLVHMQEFAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGAL 180
           LPKAEI SRV EML LVHMQEFAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGAL
Sbjct: 136 LPKAEITSRVQEMLALVHMQEFAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGAL 195

Query: 181 DKKLRDRMQLEVVDILERVGVTCVMVTHDQEEAMTMAGRIAIMNRGKFVQIGEPEEIYEH 240
           DKKLRDRMQLEVVDILERVGVTCVMVTHDQEEAMTMAGRIAIMNRGKFVQIGEPEEIYEH
Sbjct: 196 DKKLRDRMQLEVVDILERVGVTCVMVTHDQEEAMTMAGRIAIMNRGKFVQIGEPEEIYEH 255

Query: 241 PTTRYSAEFIGSVNVFEGVLKERQEDGLVLDSPGLVHPLKVDADASVVDNVPVHVALRPE 300
           PTTRYSAEFIGSVNVFEG++KERQEDGLVLDSPGL HPLKVD DASVVDNVPV VALRPE
Sbjct: 256 PTTRYSAEFIGSVNVFEGLVKERQEDGLVLDSPGLTHPLKVDPDASVVDNVPVWVALRPE 315

Query: 301 KIMLCEEPPANGCNFAVGEVIHIAYLGDLSVYHVRLKSGQMISAQLQNAHRHRKGLPTWG 360
           KIMLCE+PPA+G NFAVGEVI+IAYLGDLS+YHVRLKSGQM+SAQLQN HR+RKG PTWG
Sbjct: 316 KIMLCEDPPADGYNFAVGEVIYIAYLGDLSIYHVRLKSGQMLSAQLQNEHRYRKGAPTWG 375

Query: 361 DEVRLCWEVDSCVVLTV 377
           DEVRLCW+ DSCVVLTV
Sbjct: 376 DEVRLCWDADSCVVLTV 392


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: 624
Number of extensions: 7
Number of successful extensions: 1
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: 392
Length adjustment: 30
Effective length of query: 347
Effective length of database: 362
Effective search space:   125614
Effective search space used:   125614
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 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