GapMind for catabolism of small carbon sources

 

Alignments for a candidate for potA in Desulfotomaculum hydrothermale Lam5

Align PotG aka B0855, component of Putrescine porter (characterized)
to candidate WP_008410843.1 DESHY_RS13325 ABC transporter ATP-binding protein

Query= TCDB::P31134
         (377 letters)



>NCBI__GCF_000315365.1:WP_008410843.1
          Length = 363

 Score =  162 bits (410), Expect = 1e-44
 Identities = 102/306 (33%), Positives = 162/306 (52%), Gaps = 6/306 (1%)

Query: 19  LLEIRNLTKSYDGQHAVDDVSLTIYKGEIFALLGASGCGKSTLLRMLAGFEQPSAGQIML 78
           +L+++NL     G+  +D  +  ++KGE  AL+G +G GKS+L+++LA  E+P  G+I+ 
Sbjct: 7   ILQVKNLCWGVAGRTLIDIDNFVLHKGETIALIGPNGAGKSSLVKLLALLEKPWQGEIIF 66

Query: 79  DGVDLSQVPPYLRPINMMFQSYALFPHMTVEQNIAFGLKQDKLPKAEIASRVNEMLGLVH 138
           DG  ++  P  +R    M    AL    +V  N+A GL+   LP+ +IA RVN  L  + 
Sbjct: 67  DGRQVTGSPLQVRRQMAMVFQEALLLSGSVFGNVAQGLRFRGLPRDQIARRVNYWLKKLQ 126

Query: 139 MQEFAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRDRMQLEVVDILER 198
           +   A R    LSGG+ QRV++AR+LA  P++L LDEP  ALD   R  +  E+ +I++ 
Sbjct: 127 IAHLADRHIRYLSGGEAQRVSIARALALEPQVLFLDEPFAALDLPTRITLIEEIGEIIKA 186

Query: 199 VGVTCVMVTHDQEEAMTMAGRIAIMNRGKFVQIGEPEEIYEHPTTRYSAEFIGSVNVFEG 258
                V +TH+ EE   +AGR+  M+ GK VQ    E+I+ +P     A  +G  NV +G
Sbjct: 187 TATATVFITHNVEEIPLLAGRVCAMSAGKIVQDCSTEDIFRYPVNEEVARLVGIENVLQG 246

Query: 259 VLKERQEDGLVLDSPGLVHPLKVDADASVVDNVPVHVALRPEKIMLCEE-PPANGCNFAV 317
           V+        V ++      +   A         +++ +RPE ++L E+  P  G N   
Sbjct: 247 VVLPGGRTAQVGET-----VISFVARQDYRPGTNINLCIRPEDVILIEDRKPDGGPNLCR 301

Query: 318 GEVIHI 323
           G V  I
Sbjct: 302 GRVTKI 307


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: 311
Number of extensions: 17
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: 363
Length adjustment: 30
Effective length of query: 347
Effective length of database: 333
Effective search space:   115551
Effective search space used:   115551
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 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