GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livF in Methanospirillum lacunae Ki8-1

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_109967738.1 DK846_RS04755 ATP-binding cassette domain-containing protein

Query= uniprot:A0A165KC78
         (242 letters)



>NCBI__GCF_003173355.1:WP_109967738.1
          Length = 334

 Score = 96.7 bits (239), Expect = 5e-25
 Identities = 68/213 (31%), Positives = 110/213 (51%), Gaps = 9/213 (4%)

Query: 10  LQVKGLKVAYGGIQAVKGVDFEVREGELVSLIGSNGAGKTTTMKAITGTLSMNDGNIEYL 69
           ++++ L   YG + AV  ++  V   E+  ++G NG+GKTTT+  +T  L+ + G  E  
Sbjct: 20  IEIRDLTKNYGDLCAVNNMNLSVGN-EIFGILGPNGSGKTTTILMLTTLLAPSLGTAEIC 78

Query: 70  GKSIKGKGAWDLVKEGLVMVPEGRGVFARMTITENLQMGAYIRKDKAGILADIEKMFTIF 129
           G  I+       V+E L  VP+   V  R+T  EN+ M A +     G+    EK   + 
Sbjct: 79  GYDIQRFPR--AVRESLSYVPQDMAVDVRLTGRENVLMFAELY----GVRNPAEKTEKVL 132

Query: 130 P--RLRERKDQLAGTMSGGEQQMLAMGRALMSQPKVLLLDEPSMGLSPIMVDKIFEVVRD 187
               L +R D+ A   SGG ++ L + +AL+  PKVL LDEP++GL      KI+E +R 
Sbjct: 133 QVLELSDRADEFAKVYSGGMRRRLELAQALVHDPKVLFLDEPTVGLDVAARKKIWEHIRS 192

Query: 188 VYALGVTIVLVEQNASRALAIADRGYVMESGLI 220
           + + G++I +       A    DR  +M+ G+I
Sbjct: 193 LKSNGMSIFVTTHYMDEADRYCDRVAIMDKGVI 225


Lambda     K      H
   0.317    0.136    0.373 

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: 159
Number of extensions: 7
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: 242
Length of database: 334
Length adjustment: 26
Effective length of query: 216
Effective length of database: 308
Effective search space:    66528
Effective search space used:    66528
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 47 (22.7 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