GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_03055 in Jannaschia aquimarina GSW-M26

Align ABC transporter for L-Arginine and L-Citrulline, periplasmic substrate-binding component (characterized)
to candidate WP_043917276.1 jaqu_RS02050 transporter substrate-binding domain-containing protein

Query= reanno::pseudo1_N1B4:Pf1N1B4_3431
         (257 letters)



>NCBI__GCF_000877395.1:WP_043917276.1
          Length = 252

 Score =  189 bits (480), Expect = 5e-53
 Identities = 111/258 (43%), Positives = 162/258 (62%), Gaps = 9/258 (3%)

Query: 1   MKKLVLLGALALSVLSLPTFADEKPLKIGIEA-AYPPFASKAPDGSIVGFDYDIGNALCE 59
           MKK+V L A A    ++   A    +KIGI A AYPPFA K   G+ VG++ +I +A+C 
Sbjct: 1   MKKIVTLAAAA----AISATAATADVKIGISAEAYPPFAEKDAAGNWVGWEMEIIDAVCA 56

Query: 60  EMKVKCVWVEQEFDGLIPALKVRKIDAILSSMSITEDRKKSVDFTNKYYNTPARLVMKAG 119
            M+ +C  V   +DG+IPAL   ++DAI++SMSITE+R +++DF++KYYNTPA +V    
Sbjct: 57  AMEEECEVVPVAWDGIIPALLSGRMDAIMASMSITEERMRTIDFSDKYYNTPAVIVAAKD 116

Query: 120 TAVSENLAELKGKNIGVQRGSIHERFAREVLAPLGAEIKPYGSQNEIYLDVAAGRLDGTV 179
           + +S + A L GK +GVQ  +IH  +  +      AE+K Y + +E   D+ AGR+D  V
Sbjct: 117 SEISGDPASLDGKIVGVQVSTIHANYVEKHFEE-QAEMKVYQTFDEHNQDLVAGRVDAVV 175

Query: 180 ADATLLDDGFLKTDAGKGFAFVGPAFTDVKYFGDGVGIAVRKG-DALKDKINTAIAAIRE 238
            D+    D FL +DAG+ +   G    D + FG GVG+ +R+G D LK++ N AI  IRE
Sbjct: 176 GDSLAFQD-FLSSDAGQAYEVKG-ELNDEEVFGPGVGVGLRQGEDELKERFNAAIRQIRE 233

Query: 239 NGKYKQIQDKYFAFDIYG 256
           +G Y +I ++YF FDIYG
Sbjct: 234 DGTYDEISNRYFDFDIYG 251


Lambda     K      H
   0.318    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: 206
Number of extensions: 14
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: 257
Length of database: 252
Length adjustment: 24
Effective length of query: 233
Effective length of database: 228
Effective search space:    53124
Effective search space used:    53124
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 (21.7 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