GapMind for catabolism of small carbon sources

 

Aligments for a candidate for yjtF in Shewanella sp. ANA-3

Align Inner membrane ABC transporter permease protein YjfF (characterized)
to candidate 7024902 Shewana3_2076 inner membrane ABC transporter permease protein YjfF (RefSeq)

Query= SwissProt::P37772
         (331 letters)



>lcl|FitnessBrowser__ANA3:7024902 Shewana3_2076 inner membrane ABC
           transporter permease protein YjfF (RefSeq)
          Length = 320

 Score =  337 bits (863), Expect = 3e-97
 Identities = 175/307 (57%), Positives = 221/307 (71%)

Query: 3   KRNLPLMITIGVFVLGYLYCLTQFPGFASTRVICNILTDNAFLGIIAVGMTFVILSGGID 62
           +R +PL IT  + +  +L    QF GFAS RV+ N+L DNAFL I A+GMT VI+SGGID
Sbjct: 4   RRFIPLWITASLLLTMFLVGTFQFDGFASGRVVTNLLRDNAFLLITALGMTLVIISGGID 63

Query: 63  LSVGSVIAFTGVFLAKVIGDFGLSPLLAFPLVLVMGCAFGAFMGLLIDALKIPAFIITLA 122
           LSVG+VIA +GV  + +I ++   PLLAF ++L +G  FGA MG +I   K+  FI+TLA
Sbjct: 64  LSVGAVIALSGVVTSLLITEYQWHPLLAFVVILPLGTLFGALMGTIIHVYKLQPFIVTLA 123

Query: 123 GMFFLRGVSYLVSEESIPINHPIYDTLSSLAWKIPGGGRLSAMGLLMLAVVVIGIFLAHR 182
           GMF  RG++  +SEESI I+HP YD ++ ++  +PG G L    L+ +   VI   + H 
Sbjct: 124 GMFLARGLATTLSEESIAIDHPFYDAVAEMSIALPGNGALDLSSLIFILFFVIIAVVMHY 183

Query: 183 TRFGNQVYAIGGNATSANLMGISTRSTTIRIYMLSTGLATLAGIVFSIYTQAGYALAGVG 242
           TRFG  VYAIGGN  SA LMGIS   TTI IY +S+ LATLAGIVF+ YT +GYAL  +G
Sbjct: 184 TRFGTNVYAIGGNQHSAELMGISIAKTTISIYAISSFLATLAGIVFTFYTFSGYALGAIG 243

Query: 243 VELDAIASVVIGGTLLSGGVGTVLGTLFGVAIQGLIQTYINFDGTLSSWWTKIAIGILLF 302
           VELDAIA+VVIGGTLL+GG G VLGT+ GV + G+IQTYI FDG+LSSWWTKI IG+LLF
Sbjct: 244 VELDAIAAVVIGGTLLTGGSGFVLGTVLGVILMGVIQTYITFDGSLSSWWTKIVIGLLLF 303

Query: 303 IFIALQR 309
            FI LQ+
Sbjct: 304 FFILLQK 310


Lambda     K      H
   0.329    0.145    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: 396
Number of extensions: 20
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: 331
Length of database: 320
Length adjustment: 28
Effective length of query: 303
Effective length of database: 292
Effective search space:    88476
Effective search space used:    88476
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 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, the preprint on GapMind for carbon sources, 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