GapMind for catabolism of small carbon sources

 

Alignments for a candidate for yjtF in Pseudomonas fluorescens FW300-N2E3

Align Inner membrane ABC transporter permease protein YjfF (characterized)
to candidate AO353_21390 AO353_21390 ABC transporter

Query= SwissProt::P37772
         (331 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_21390
          Length = 340

 Score =  131 bits (329), Expect = 3e-35
 Identities = 105/327 (32%), Positives = 170/327 (51%), Gaps = 32/327 (9%)

Query: 3   KRNLPLMITIGVFVLGYLYCLTQFPGFA--------STRVICNILTDNAFLGIIAVGMTF 54
           +R LP  ++I + ++G       F            S R++  IL   + +G++A+G+T 
Sbjct: 17  RRRLPTELSIFLVLIGIGLVFEMFGWIVRDQSFLMNSQRLVLMIL-QVSIIGLLAIGVTQ 75

Query: 55  VILSGGIDLSVGSVIAFTGVFLAKVI--GDFGLS--PLLA-----FPLV--LVMGCAFGA 103
           VI++ GIDLS GSV+A + +  A +    DF  +  P L       P++  L +G   GA
Sbjct: 76  VIITTGIDLSSGSVLALSAMIAASLAQTSDFARAVFPSLTDLPVWIPVIAGLGVGLLAGA 135

Query: 104 FMGLLIDALKIPAFIITLAGMFFLRGVSYLVSEESIPINHPIYDTLSSLAWKIPGGGRLS 163
             G +I    IP FI TL  M   RG++   +E       P+  ++ S ++   G G   
Sbjct: 136 INGSIIAVTGIPPFIATLGMMVSARGLARYYTE-----GQPV--SMLSDSYTAIGHG--- 185

Query: 164 AMGLLMLAVVVIGIFLAHR-TRFGNQVYAIGGNATSANLMGISTRSTTIRIYMLSTGLAT 222
           AM +++  VV +   +A R T++G   YAIGGN  +A   GI+ +   + +Y ++  LA 
Sbjct: 186 AMPVIIFLVVAVIFHIALRYTKYGKYTYAIGGNMQAARTSGINVKRHLVIVYSIAGLLAG 245

Query: 223 LAGIVFSIYTQAGYALAGVGVELDAIASVVIGGTLLSGGVGTVLGTLFGVAIQGLIQTYI 282
           LAG+V S     G A  G+  ELDAIA+ VIGGT L+GGVG + GT+ G  I G++ +  
Sbjct: 246 LAGVVASARAATGQAGMGMSYELDAIAAAVIGGTSLAGGVGRITGTVIGALILGVMASGF 305

Query: 283 NFDGTLSSWWTKIAIGILLFIFIALQR 309
            F G + ++   I  G+++ I + + +
Sbjct: 306 TFVG-VDAYIQDIIKGLIIVIAVVIDQ 331


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: 345
Number of extensions: 28
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: 331
Length of database: 340
Length adjustment: 28
Effective length of query: 303
Effective length of database: 312
Effective search space:    94536
Effective search space used:    94536
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 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