GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruF in Sinorhizobium meliloti 1021

Align Fructose import permease protein FruF (characterized)
to candidate SM_b21343 SM_b21343 sugar uptake ABC transporter permease

Query= SwissProt::Q8G846
         (356 letters)



>FitnessBrowser__Smeli:SM_b21343
          Length = 334

 Score =  184 bits (468), Expect = 2e-51
 Identities = 116/317 (36%), Positives = 183/317 (57%), Gaps = 25/317 (7%)

Query: 24  SIVAFILLVIICTIFQHDFLALSWNSNTGGLAGPLITMLQESARYLMIATGMTLVISTAG 83
           ++ AF+ L++   +F  +FL+L            L   L + A  +++A GMTLVI+T G
Sbjct: 28  TVAAFLALILFNVVFTPNFLSLQ----------TLNVNLTQVATIVIVAIGMTLVIATGG 77

Query: 84  IDLSVGSVMAVAGAAA----MQTLSNGMNVWLSILIA-----LAVGLAIGCVNGALVSFL 134
           IDLSVGS+MA+ GA A    M TL    ++ +++ +A     +A GL +G  NG LV+  
Sbjct: 78  IDLSVGSLMAIGGALAPMIFMGTLFPVSSMPVAVALAFVLPVVATGL-LGLFNGLLVTRF 136

Query: 135 GLQPFITTLIMMLAGRGMAKVITSGENTDASAVAGNEPLKWFANGFILGIPANFVIAVII 194
            +QP I TL++ +AGRG+A+V+T+G       V  NE  ++ A G + GIPA  ++ + I
Sbjct: 137 AIQPIIATLVLFIAGRGIAQVMTNGN----LQVFRNEGFQFIALGRVAGIPAQVILMIAI 192

Query: 195 VILVGLLCRKTAMGMMIEAVGINQEASRMTGIKPKKILFLVYAISGFLAAIAGLFATASV 254
             +     R T  G  + AVG N++ASR+TGI   ++  LVY ISG LA +AGL   A  
Sbjct: 193 AAIAWAAIRYTVFGRQVIAVGGNEKASRLTGIPVHRVKLLVYMISGALAGVAGLIVVARN 252

Query: 255 MRVDVVKTGQDLEMYAILAVVIGGTSLLGGKFSLAGSAVGAVIIAMIRKTIITLGV-NAE 313
              D    G  +E+ AI AV +GGT L GG+ ++ G+ +GA++I ++R T++  GV +A 
Sbjct: 253 SASDANLVGLGMELDAIAAVAVGGTLLTGGRANIVGTVIGALVIQLVRYTLLANGVPDAA 312

Query: 314 ATPAFFAVVVIVICVMQ 330
           A     A++++ + + Q
Sbjct: 313 ALIVKAALILLAVFIQQ 329


Lambda     K      H
   0.325    0.136    0.384 

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: 335
Number of extensions: 17
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: 356
Length of database: 334
Length adjustment: 29
Effective length of query: 327
Effective length of database: 305
Effective search space:    99735
Effective search space used:    99735
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 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