GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SM_b21216 in Shewanella loihica PV-4

Align ABC transporter for D-Glucosamine, ATPase component (characterized)
to candidate 5208351 Shew_0863 ABC transporter-related protein (RefSeq)

Query= reanno::Smeli:SM_b21216
         (360 letters)



>FitnessBrowser__PV4:5208351
          Length = 342

 Score =  184 bits (468), Expect = 2e-51
 Identities = 113/301 (37%), Positives = 168/301 (55%), Gaps = 17/301 (5%)

Query: 1   MSALEIRNIRKRYGEVETLKGIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSGGDI 60
           MS L I  +   Y     L+G+D+ L  GE   LLG SGCGK+TLL  IAGL   S G I
Sbjct: 1   MSTLTIEQVHSDYQGQTILRGLDLVLHQGEIAALLGPSGCGKTTLLKAIAGLQPISQGRI 60

Query: 61  LIGERSVLG----VHPKDRDIAMVFQSYALYPNLSVARNIGFGLEMRRVPQAEHDKAVRD 116
            I  R + G    V  + R++ M+FQ YAL+P+L+VA NI FG+  + + +A     + +
Sbjct: 61  SINGRLLSGPETFVPSERREVGMIFQDYALFPHLTVAENILFGV--KGLDKAARQARLGE 118

Query: 117 TARLLQIENLLDRKPSQLSGGQRQRVAIGRALVRNPQVFLFDEPLSNLDAKLRMEMRTEL 176
              L+++E L  R P +LSGGQ+QRV+I RAL   P++ L DEP SN+DAK+R EM  E+
Sbjct: 119 MLALVKLEGLGGRYPHELSGGQQQRVSIARALAYEPELLLLDEPFSNIDAKVRGEMMVEI 178

Query: 177 KRLHQMLRTTVVYVTHDQIEAMTLATRIAVMRDGRIEQLAAPDEVYDRPATLYVAGFVGS 236
           + + +    + V+VTH + EA   A ++A+ +DG I Q  + + +Y  P   YVA F+G 
Sbjct: 179 REILKQRGVSAVFVTHSKDEAFVFADKLALFKDGGIAQYGSAESLYAEPTDKYVAEFLGQ 238

Query: 237 PPMNILDAEMTANG---LKIEGCEEVLPLPAAFNGAAWAGRRVKVGIRPEALRLAAGSEA 293
             +N L  E+         +   +    LP A      AG R ++ +RPE L++A   + 
Sbjct: 239 --VNYLSCEVKDRARLQTLLGEVQSSSDLPKA------AGYRGELLLRPEQLQMAGDEQG 290

Query: 294 Q 294
           +
Sbjct: 291 E 291


Lambda     K      H
   0.320    0.136    0.385 

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: 278
Number of extensions: 18
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: 360
Length of database: 342
Length adjustment: 29
Effective length of query: 331
Effective length of database: 313
Effective search space:   103603
Effective search space used:   103603
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (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