GapMind for catabolism of small carbon sources

 

Alignments for a candidate for yjtF in Tistlia consotensis USBA 355

Align Inner membrane ABC transporter permease protein YjfF (characterized)
to candidate WP_085121058.1 B9O00_RS01465 ABC transporter permease

Query= SwissProt::P37772
         (331 letters)



>NCBI__GCF_900177295.1:WP_085121058.1
          Length = 335

 Score =  148 bits (373), Expect = 2e-40
 Identities = 110/307 (35%), Positives = 169/307 (55%), Gaps = 15/307 (4%)

Query: 4   RNLPLMITIGVFVLGYLYCLTQFPGFASTRVICNILTDNAFLGIIAVGMTFVILSGGIDL 63
           R L L + IG  VL  L      P F +   I NIL  +  +GI+++GMTFVIL+GGIDL
Sbjct: 35  RMLGLALVIGA-VLSLLS-----PYFLTESNIFNILDQSVVIGILSIGMTFVILTGGIDL 88

Query: 64  SVGSVIAFTGVFLAKVIGDFGLSPLLAFPLVLVMGCAFGAFMGLLIDALKIPAFIITLAG 123
           SVGSV   +G+ L   + D+ +   +A  L ++ G   G   G+LI   ++ AF++TL  
Sbjct: 89  SVGSVAGLSGIVLGLALKDYPIP--VAILLGVLTGAGVGLVSGILIGYFRLAAFVVTLGM 146

Query: 124 MFFLRGVSYLVSEESIPINHPIYDTLSSLAWKIPGGGRLSAMGLLMLAVVVIGIFLAHRT 183
           M   R ++Y+ S ++     P    LSS+ +    G   + +  L  A ++   +L + T
Sbjct: 147 MAIGRSLAYIFSGQTAISGFP--SDLSSIVYTDVFGIPTNVL-FLGFAYLLAWGYLTY-T 202

Query: 184 RFGNQVYAIGGNATSANLMGISTRSTTIRIYMLSTGLATLAGIVFSIYTQAGY-ALAGVG 242
           + G  +YAIG N  +A   G+     +I  Y++S  LA +A I FS+        L G G
Sbjct: 203 KGGRTIYAIGSNKEAARAAGLGVLFYSILPYVVSGALAAVA-ITFSVAQILSVDPLTGNG 261

Query: 243 VELDAIASVVIGGTLLSGGVGTVLGTLFGVAIQGLIQTYINFDGTLSSWWTKIAIGILLF 302
           +ELDAIA+VVIGG  L GG G+++GTL GV I  +I+  +N  G +S +W   AIG ++ 
Sbjct: 262 MELDAIAAVVIGGASLYGGRGSIVGTLIGVLIMVMIRNGLNLLG-VSPFWQGSAIGSIII 320

Query: 303 IFIALQR 309
           + + ++R
Sbjct: 321 MALLVER 327


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: 350
Number of extensions: 36
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: 331
Length of database: 335
Length adjustment: 28
Effective length of query: 303
Effective length of database: 307
Effective search space:    93021
Effective search space used:    93021
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: 49 (23.5 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