GapMind for catabolism of small carbon sources

 

Alignments for a candidate for artJ in Jannaschia aquimarina GSW-M26

Align AotJ aka PA0888, component of Arginine/ornithine (but not lysine) porter (characterized)
to candidate WP_043917276.1 jaqu_RS02050 transporter substrate-binding domain-containing protein

Query= TCDB::O50181
         (259 letters)



>NCBI__GCF_000877395.1:WP_043917276.1
          Length = 252

 Score =  195 bits (496), Expect = 7e-55
 Identities = 110/258 (42%), Positives = 161/258 (62%), Gaps = 8/258 (3%)

Query: 1   MKKLALLGALALSVLSLPTFAADKPVRIGIEA-AYPPFSLKTPDGQLAGFDVDIGNALCE 59
           MKK+  L A A    ++   AA   V+IGI A AYPPF+ K   G   G++++I +A+C 
Sbjct: 1   MKKIVTLAAAA----AISATAATADVKIGISAEAYPPFAEKDAAGNWVGWEMEIIDAVCA 56

Query: 60  EMKVQCKWVEQEFDGLIPALKVRKIDAILSSMTITDERKRSVDFTNKYYNTPARFVMKEG 119
            M+ +C+ V   +DG+IPAL   ++DAI++SM+IT+ER R++DF++KYYNTPA  V  + 
Sbjct: 57  AMEEECEVVPVAWDGIIPALLSGRMDAIMASMSITEERMRTIDFSDKYYNTPAVIVAAKD 116

Query: 120 ASLNDPKADLKGKKAGVLRGSTADRYASAELTPAGVEVVRYNSQQEANMDLVAGRLDAVV 179
           + ++   A L GK  GV   +    Y          E+  Y +  E N DLVAGR+DAVV
Sbjct: 117 SEISGDPASLDGKIVGVQVSTIHANYVEKHFEEQ-AEMKVYQTFDEHNQDLVAGRVDAVV 175

Query: 180 ADSVNLEDGFLKTDAGKGYAFVGPQLTDAKYFGEGVGIAVRKGDSELAGKFNAAIDALRA 239
            DS+  +D FL +DAG+ Y   G +L D + FG GVG+ +R+G+ EL  +FNAAI  +R 
Sbjct: 176 GDSLAFQD-FLSSDAGQAYEVKG-ELNDEEVFGPGVGVGLRQGEDELKERFNAAIRQIRE 233

Query: 240 NGKYKQIQDKYFSFDVYG 257
           +G Y +I ++YF FD+YG
Sbjct: 234 DGTYDEISNRYFDFDIYG 251


Lambda     K      H
   0.316    0.135    0.381 

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: 218
Number of extensions: 10
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: 259
Length of database: 252
Length adjustment: 24
Effective length of query: 235
Effective length of database: 228
Effective search space:    53580
Effective search space used:    53580
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 (21.6 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