GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livM in Dinoroseobacter shibae DFL-12

Align ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate 3606951 Dshi_0379 inner-membrane translocator (RefSeq)

Query= TCDB::Q8DQH9
         (318 letters)



>FitnessBrowser__Dino:3606951
          Length = 358

 Score =  133 bits (334), Expect = 7e-36
 Identities = 97/320 (30%), Positives = 168/320 (52%), Gaps = 36/320 (11%)

Query: 19  YSLISVLVSV--GVLNLFYVQ-ILQQIGINIILAVGLNLIVGFSGQFSLGHAGFMAIGAY 75
           Y +++V V +   V+N ++   ++    I  I A+GLN++ G+ GQ SLG  GFMA+GAY
Sbjct: 30  YLVLAVAVGIIPFVINDYWASAVMVPFLIWAIAAIGLNILTGYCGQVSLGTGGFMAVGAY 89

Query: 76  AAAIIGSKSPTYGAFFGAMLVGALLSGAVALLVGIPTLRLKGDYLAVATLGVSEIIRIFI 135
           A   + +  P        +L+G +++ AV +L G+P+LR+KG YLAVATL  ++   +++
Sbjct: 90  ACYKLMTAFPDLNIAI-CVLLGGVITAAVGVLFGLPSLRIKGFYLAVATL-AAQFFLVWL 147

Query: 136 IN--GGSLTNGAAGILGIPNFTTW-------------QMVYFFVVITTIATL--NFLRSP 178
            N         A+G +  P  T +             + ++    +  +A L  N  R  
Sbjct: 148 FNKVPWFYNYSASGQINAPERTMFGYAITGPNADAAPKYLFCLAFLFVLAWLARNLTRGT 207

Query: 179 IGRSTLSVREDEIAAESVGVNTTKIKIIAFVFGAITASIAGSL-QAGFIGSV-VPKDYTF 236
           IGRS +++R+ +IAAE +GVN  K K+ AF   +    +AG+L  + ++G+V V + +  
Sbjct: 208 IGRSWMAIRDMDIAAEIIGVNPLKAKLTAFAVSSFFVGVAGALFFSVYLGAVEVGEAFGI 267

Query: 237 INSINVLIIVVFGGLGSITGAIVSAIVLGILNMLLQDV------------ASVRMIIYAL 284
             S  VL +++ GGLGSI G++  A  + +L +LL++V            A    ++   
Sbjct: 268 NQSFLVLFMIIIGGLGSIFGSLAGAAFIVLLPVLLKNVMVGSLGWDTAIAAHFEFVVLGG 327

Query: 285 ALVLVMIFRPGGLLGTWELS 304
            ++  +I  P GL   W+L+
Sbjct: 328 LIIFFLIVEPHGLARLWQLA 347


Lambda     K      H
   0.327    0.143    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: 271
Number of extensions: 13
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: 318
Length of database: 358
Length adjustment: 28
Effective length of query: 290
Effective length of database: 330
Effective search space:    95700
Effective search space used:    95700
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 (21.6 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 17 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