GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ybhL in Catellicoccus marimammalium M35/04/3

Align The YbhL (AceP) protein. Possibly a pmf-dependent acetate uptake transporter. [14C]Acetate uptake was inhibited by CCCP as well as cold acetate, serine, α-ketoglutarate, lactate, and succinate (M. Inouye, personal communication) (characterized)
to candidate WP_009491941.1 C683_RS05740 Bax inhibitor-1/YccA family protein

Query= TCDB::P0AAC4
         (234 letters)



>NCBI__GCF_000313915.1:WP_009491941.1
          Length = 234

 Score =  119 bits (299), Expect = 4e-32
 Identities = 77/216 (35%), Positives = 120/216 (55%), Gaps = 5/216 (2%)

Query: 16  GLQTYMAQVYGWMTVGLLLTAFVAWYAANSAAVMELLFTNRVFL-IGLIIAQLALVIVLS 74
           GL  +  +VY  + +G+ ++A V++        + + F N   L I L I ++ LVI   
Sbjct: 12  GLNRFFGEVYAKVALGVGVSALVSFILIYFMPNVLVAFANSTILWIVLCIVEIMLVISAG 71

Query: 75  AMIQKLSAGVTTMLFMLYSALTGLTLS-SIFIVYTAASIASTFVVTAGMFGAMSLYGYTT 133
                 ++  T M++M+YS +  LTL+  + IV +   IA  F+VTA MF AMS+YG TT
Sbjct: 72  HRAYSGNSSGTMMMYMVYSIINALTLTVGLTIVSSPKVIAQAFLVTALMFVAMSIYGRTT 131

Query: 134 KRDLSGFGNMLFMALIGIVLASLVNFWLKSEALMWAVTYIGVIVFVGLTAYDTQKLKNMG 193
           KRDLS + N L    +G+++  LVN  L S AL +  + + V +F G  AYDTQ +  + 
Sbjct: 132 KRDLSAWRNFLMGISLGVIITLLVNLILGSGALSFFCSLVSVALFAGYMAYDTQMIIRLY 191

Query: 194 EQIDTRDTSNLRKYSILGALTLYLDFINLFLMLLRI 229
           +  ++   S L  Y   GA+ LY+D I +F+ LL+I
Sbjct: 192 QMANSETKSGLATY---GAMNLYMDLIAMFINLLQI 224


Lambda     K      H
   0.330    0.140    0.403 

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: 179
Number of extensions: 12
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: 234
Length of database: 234
Length adjustment: 23
Effective length of query: 211
Effective length of database: 211
Effective search space:    44521
Effective search space used:    44521
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 46 (22.3 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