GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araZsh in Sinorhizobium meliloti 1021

Align Inner-membrane translocator (characterized, see rationale)
to candidate SM_b21590 SM_b21590 inner membrane ABC transporter permease YjfF

Query= uniprot:A0KWY7
         (320 letters)



>FitnessBrowser__Smeli:SM_b21590
          Length = 322

 Score =  348 bits (892), Expect = e-100
 Identities = 174/307 (56%), Positives = 228/307 (74%)

Query: 4   RRFIPLWITASLLLTMFLVGTFQFDGFASGRVVTNLLRDNAFLLITALGMTLVIISGGID 63
           ++++PL  T  + +  + +   Q+    S RV+ NLL DNAFL I A+GMT VI+SGGID
Sbjct: 3   QKYLPLTATILIFVLSYALCVAQYPNMLSTRVIGNLLTDNAFLGIAAVGMTFVILSGGID 62

Query: 64  LSVGAVIALSGVVTSLLITEYQWHPLLAFVVILPLGTLFGALMGTIIHVYKLQPFIVTLA 123
           LS+GAVIA +GV  ++++     HPL+AF ++L + TLFGALMG IIH  ++  FIVTLA
Sbjct: 63  LSIGAVIAFAGVFLAVVLEHGGMHPLVAFALLLAITTLFGALMGAIIHYLEMPAFIVTLA 122

Query: 124 GMFLARGLATTLSEESIAIDHPFYDAVAEMSIALPGNGALDLSSLIFILFFVIIAVVMHY 183
           GMFLARG+A  LS +SI I HPFY  +  +   LPG G + L   + +  F +  ++ H 
Sbjct: 123 GMFLARGMAFVLSIDSIPIKHPFYATLKSLYFKLPGGGRITLIGGLMLFVFAVGILIAHR 182

Query: 184 TRFGTNVYAIGGNQHSAELMGISIAKTTISIYAISSFLATLAGIVFTFYTFSGYALGAIG 243
           TRFGTN+YA+GG   +A+LMG+ +A TTI IYA+S  LA L+GIVF+ YT +GY+L A+G
Sbjct: 183 TRFGTNIYALGGGTATAKLMGVPVAATTIRIYALSGLLAGLSGIVFSLYTSAGYSLAAVG 242

Query: 244 VELDAIAAVVIGGTLLTGGSGFVLGTVLGVILMGVIQTYITFDGSLSSWWTKIVIGLLLF 303
           VELDAI AVVIGGTLLTGGSGFV GT++G+++ G+IQTYITFDG+LSSWWTKI+IGLLLF
Sbjct: 243 VELDAITAVVIGGTLLTGGSGFVAGTLVGILIQGLIQTYITFDGTLSSWWTKILIGLLLF 302

Query: 304 FFILLQK 310
            FILLQK
Sbjct: 303 AFILLQK 309


Lambda     K      H
   0.330    0.145    0.424 

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: 474
Number of extensions: 27
Number of successful extensions: 1
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: 320
Length of database: 322
Length adjustment: 28
Effective length of query: 292
Effective length of database: 294
Effective search space:    85848
Effective search space used:    85848
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 (21.8 bits)
S2: 48 (23.1 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