GapMind for catabolism of small carbon sources

 

Aligments for a candidate for PS417_17595 in Desulfovibrio vulgaris Miyazaki F

Align ABC transporter permease subunit; SubName: Full=Amino acid ABC transporter permease; SubName: Full=Histidine transport system permease protein (characterized, see rationale)
to candidate 8501185 DvMF_1919 polar amino acid ABC transporter, inner membrane subunit (RefSeq)

Query= uniprot:A0A1N7UBU2
         (233 letters)



>lcl|FitnessBrowser__Miya:8501185 DvMF_1919 polar amino acid ABC
           transporter, inner membrane subunit (RefSeq)
          Length = 223

 Score =  114 bits (284), Expect = 2e-30
 Identities = 68/214 (31%), Positives = 105/214 (49%), Gaps = 10/214 (4%)

Query: 12  PMLAQGAWMTLKLAFLALALSLALGLIAAAAKLSSAKWLRVPATLYTTLIRSVPDLVLIL 71
           P+L  G  +T+ +    LA+   LG     AK +  K  R  A +Y   IR  P +V ++
Sbjct: 15  PLLLGGVHLTIIITLGGLAIGFLLGTATGLAKTARGKLPRALADIYVEAIRGTPLIVQVM 74

Query: 72  LIFYSLQLWLNDLSEVFGWDYFEIDPFTAGVITLGFIYGAYFTENFRGAILSVPVGQLEA 131
            +++ + L               I P TAG+I +    GAY  E  RGA+ S+ VGQ EA
Sbjct: 75  FLYFGVPLATG----------MRIPPVTAGIIAIAVNSGAYIAEIVRGAVESIDVGQTEA 124

Query: 132 ATAYGLSRWQRFHLVLFPQLMRFALPGLGNNWLVLLKSTALVSIIGLSDLVKAAQNAGKT 191
             + GL+R Q    V++PQ  R  +P LGN +++ LK T+L+ +IG+ +L +  Q     
Sbjct: 125 GRSIGLTRMQTLLYVVWPQAFRRMIPPLGNQFIISLKDTSLLVVIGVGELTRQGQEIIAV 184

Query: 192 TNEPLYFLILAGLMYLVITTLSNRVLKRLERRYN 225
                   +   +MYLV+T    R L+  ER+ N
Sbjct: 185 NFRAFEVWLTVAVMYLVMTLSIARALRVYERKLN 218


Lambda     K      H
   0.327    0.141    0.428 

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: 105
Number of extensions: 4
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: 233
Length of database: 223
Length adjustment: 23
Effective length of query: 210
Effective length of database: 200
Effective search space:    42000
Effective search space used:    42000
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 (21.7 bits)
S2: 46 (22.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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