GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natE in Methylocystis bryophila S285

Align NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate WP_085770499.1 B1812_RS04360 ABC transporter ATP-binding protein

Query= TCDB::P73650
         (240 letters)



>NCBI__GCF_002117405.1:WP_085770499.1
          Length = 266

 Score =  160 bits (406), Expect = 2e-44
 Identities = 93/241 (38%), Positives = 145/241 (60%), Gaps = 9/241 (3%)

Query: 4   LLVVKDVFAGYVADVPILQGINFSIAPGELVTVIGPNGAGKSTLAKTIFGLLTPSQGEI- 62
           LL ++DV A Y   +  L+ ++  +  GE+V ++G NG+GK+T+      LL   +G+I 
Sbjct: 7   LLELRDVEASYNQAIVALRDVSLKVRRGEIVALLGANGSGKTTILNATSRLLAAERGQIT 66

Query: 63  ----IFKGENITGLGSDQIVRRGMCYVPQVCNVFGSLTVAENLDMGAFLHQGPTQTLKDR 118
               +F G + +   + ++ ++G+  V +   VF SLTV ENL  GA   +   + L+D 
Sbjct: 67  SGKILFDGRSTSKSSTAELAQKGLVQVLEGRRVFRSLTVEENLASGALARRSNRRELRDD 126

Query: 119 ---IYTMFPKLAQRRNQRAGTLSGGERQMLAMGRALMLDPDLLLLDEPSAALSPILVKDV 175
              +Y +FP+L  RR   AG LSGGE+QM A+GRA+M  P LL+LDEPS  L+P++V+++
Sbjct: 127 LDYVYGVFPQLKHRRRSLAGLLSGGEQQMTAIGRAMMTHPRLLILDEPSMGLAPLVVEEI 186

Query: 176 FAQIKAIN-ATGKAIILVEQNAKQALMMADRGYVLENGRDKLEGSGQSLLNDPLVGELYL 234
           +  + A+N   G ++++ EQNA  AL  A RGYV+ENG   LEG+  +L     V + YL
Sbjct: 187 YQVLGALNRMKGLSLLVAEQNAYVALRHAHRGYVVENGVVVLEGAAATLQEREDVKDFYL 246

Query: 235 G 235
           G
Sbjct: 247 G 247


Lambda     K      H
   0.320    0.139    0.393 

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: 170
Number of extensions: 7
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: 240
Length of database: 266
Length adjustment: 24
Effective length of query: 216
Effective length of database: 242
Effective search space:    52272
Effective search space used:    52272
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: 46 (22.3 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