GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacJ in Shewanella loihica PV-4

Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate 5208351 Shew_0863 ABC transporter-related protein (RefSeq)

Query= uniprot:D4GP38
         (383 letters)



>FitnessBrowser__PV4:5208351
          Length = 342

 Score =  189 bits (480), Expect = 1e-52
 Identities = 121/346 (34%), Positives = 190/346 (54%), Gaps = 33/346 (9%)

Query: 22  LSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGDIYIGGDHMN----YRVPQNRDI 77
           L L +   E   L+GPSGCGK+T L+ +AGL+  + G I I G  ++    +   + R++
Sbjct: 22  LDLVLHQGEIAALLGPSGCGKTTLLKAIAGLQPISQGRISINGRLLSGPETFVPSERREV 81

Query: 78  AMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVVEVAETLGIADLLDRKPDELSG 137
            M+FQDYAL+PH+TV +NI FG++   G   A R  R+ E+   + +  L  R P ELSG
Sbjct: 82  GMIFQDYALFPHLTVAENILFGVK---GLDKAARQARLGEMLALVKLEGLGGRYPHELSG 138

Query: 138 GQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQNLQDQLAVTTVYVTHNQTE 197
           GQQQRV++ RA+  +PE+ L+DEP SN+DAK+R EM  E++ +  Q  V+ V+VTH++ E
Sbjct: 139 GQQQRVSIARALAYEPELLLLDEPFSNIDAKVRGEMMVEIREILKQRGVSAVFVTHSKDE 198

Query: 198 AMTMADRIAVMDDGELQQVASPFECYHEPNNLFVAEFIGEPMINL----VRGTRSESTFV 253
           A   AD++A+  DG + Q  S    Y EP + +VAEF+G+  +N     V+      T +
Sbjct: 199 AFVFADKLALFKDGGIAQYGSAESLYAEPTDKYVAEFLGQ--VNYLSCEVKDRARLQTLL 256

Query: 254 GEHFSYPLDEDVMESVDDRDDFVLGVRPEDIEVADAAPDDAALDDHDLQMDVTVVEPHGD 313
           GE  S     D+ ++   R + +L  RPE +++A            D Q + T++     
Sbjct: 257 GEVQS---SSDLPKAAGYRGELLL--RPEQLQMAG-----------DEQGEGTIIARRFL 300

Query: 314 QNVLHLSHPDQPSADDALQAVTEGMHLVTRGDRVTVTIPPDKIHLF 359
            N+ H S        + + AV   +H  + G +V +++ P    LF
Sbjct: 301 GNLCHYS----ILIGEEILAVRSPLHHFSPGQKVGLSVTPHPAVLF 342


Lambda     K      H
   0.317    0.135    0.386 

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: 291
Number of extensions: 8
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: 383
Length of database: 342
Length adjustment: 29
Effective length of query: 354
Effective length of database: 313
Effective search space:   110802
Effective search space used:   110802
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (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