GapMind for catabolism of small carbon sources

 

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

Align ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate WP_109968112.1 DK846_RS06435 ATP-binding cassette domain-containing protein

Query= TCDB::Q8DQH7
         (236 letters)



>NCBI__GCF_003173355.1:WP_109968112.1
          Length = 312

 Score =  127 bits (318), Expect = 3e-34
 Identities = 79/232 (34%), Positives = 133/232 (57%), Gaps = 16/232 (6%)

Query: 2   SVLKVENLSVHYGMIQAVRDVSFEVNEGEVVSLIGANGAGKTTILRTLSGLVRPSSGKIE 61
           ++++V N S  YG ++AV+D+SF+V +GEV S +G NGAGK+T++ +L  L+    G ++
Sbjct: 4   NIVEVSNFSYSYGELEAVKDISFQVKKGEVFSFLGPNGAGKSTVINSLITLLPLQKGTVQ 63

Query: 62  FLGQEIQKMPAQKIVAGGLSQVPEGRHVFPGLTVMENLE-------MGAFLKKNREENQA 114
             G +++    Q+ V   +  V +   +   +TV E LE       MG   KKNR     
Sbjct: 64  IAGYDLRT--EQENVRQSIGIVFQKITLDKDMTVRETLEFHGSIYLMGGAEKKNRIIELL 121

Query: 115 NLKKVFSRFPRLEERKNQDAATLSGGEQQMLAMGRALMSTPKLLLLDEPSMGLAPIFIQE 174
            L +       L E+ +   +TLSGG ++ L + R LM+ PK+L LDEP++GL P   ++
Sbjct: 122 KLVE-------LTEKADVLVSTLSGGMKRRLEIARGLMTRPKVLFLDEPTIGLDPQTRRK 174

Query: 175 IFDIIQDIQKQGTTVLLIEQNANKALAISDRGYVLETGKIVLSGTGKELASS 226
            ++ ++ + ++GTTV L     ++A  +SD+  +++ GKIV+ GT  EL  S
Sbjct: 175 TWEYLRSVNEEGTTVFLTTHYMDEADLLSDQIALIDHGKIVIQGTPAELKQS 226


Lambda     K      H
   0.315    0.134    0.358 

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: 169
Number of extensions: 10
Number of successful extensions: 2
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: 236
Length of database: 312
Length adjustment: 25
Effective length of query: 211
Effective length of database: 287
Effective search space:    60557
Effective search space used:    60557
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: 42 (22.0 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