GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS00895 in Trichormus variabilis ATCC 29413

Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate WP_011321041.1 AVA_RS22160 urea ABC transporter ATP-binding protein UrtD

Query= uniprot:D8J1T6
         (255 letters)



>NCBI__GCF_000204075.1:WP_011321041.1
          Length = 246

 Score =  157 bits (398), Expect = 1e-43
 Identities = 91/252 (36%), Positives = 144/252 (57%), Gaps = 8/252 (3%)

Query: 1   MSQTLLKIRDVSKRFGGLQALNGVGITIERGQIYGLIGPNGAGKTTFFNVITGLYQPDTG 60
           M+  +L+  +V+  F G +ALN +  +++ G++  +IGPNGAGKTTF +VITG  QP  G
Sbjct: 1   MNAKILETENVTVSFDGFKALNQLNFSMDVGELRVVIGPNGAGKTTFLDVITGKVQPTIG 60

Query: 61  TFELDGKPYSPSAPHEVAKAGIARTFQNIRLFGEMTVLENVMVGCHVRTKQNVFGAVFRH 120
                GK       H++A+ GI R FQ  R++  +T  EN+ +  +    +NVF  +F  
Sbjct: 61  RVLFKGKNLRSLREHQIARRGIGRKFQTPRVYLNLTPRENLEITSN--RNKNVFSTLFGR 118

Query: 121 KAAREEEAAIREKSQKLLDFVGIGQFAKRTARHLSYGDQRRLEIARALATDPQLLALDEP 180
               EE +      + LL+ +G+   A   A  LS+G+++RLEI   +   P LL +DEP
Sbjct: 119 SQPTEENSI-----KGLLETIGLTPKADIPAALLSHGEKQRLEIGMLVGQSPDLLLVDEP 173

Query: 181 AAGMNATEKLGLRELLVKIQAEGKTILLIEHDVKLMMGLCNRITVLDYGKPIAEGVPADV 240
            AG+   E   + ELL+ + A+  +IL+IEHD++ +  +  ++TVL  G  + EG   +V
Sbjct: 174 VAGLTDEETYNIGELLLTL-AQSHSILVIEHDMEFVRQIAKKVTVLHEGSVLCEGNFEEV 232

Query: 241 QKNPAVIEAYLG 252
           Q +P V+E YLG
Sbjct: 233 QSDPRVVEVYLG 244


Lambda     K      H
   0.320    0.138    0.394 

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: 161
Number of extensions: 8
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: 255
Length of database: 246
Length adjustment: 24
Effective length of query: 231
Effective length of database: 222
Effective search space:    51282
Effective search space used:    51282
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