GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aatP in Dinoroseobacter shibae DFL-12

Align Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized)
to candidate 3607933 Dshi_1341 ABC transporter related (RefSeq)

Query= TCDB::P0AAG3
         (241 letters)



>FitnessBrowser__Dino:3607933
          Length = 362

 Score =  152 bits (385), Expect = 7e-42
 Identities = 89/226 (39%), Positives = 128/226 (56%), Gaps = 5/226 (2%)

Query: 15  QVLTDCSTEVKKGEVVVVCGPSGSGKSTLIKTVNGLEPVQQGEITVDGIVVNDKKTDLAK 74
           +V+ D S  V  G+V  + GPSG GKST ++ + G++    G +TVDG VV+     L  
Sbjct: 22  RVVDDVSIRVMPGQVTCLLGPSGCGKSTTLRIIAGVDRQDSGTLTVDGEVVSSDDIHLPP 81

Query: 75  LRSRVGMVFQHFELFPHLSIIENLTLAQVKVLKRDKAPAREKALKLLERVGLSAHANKFP 134
               VG++FQ F LFPHL + +N+       L   +   R +A +LL+RVGL   A KFP
Sbjct: 82  EARSVGLMFQDFALFPHLCVADNVGFG----LSGSRKEKRARAHELLDRVGLLGDAGKFP 137

Query: 135 AQLSGGQQQRVAIARALCMDPIAMLFDEPTSALDPEMINEVLDVMVE-LANEGMTMMVVT 193
            QLSGG+QQRVA+ARA+   P  ML DEP S LD  + + + D  +E L +EG  +++VT
Sbjct: 138 HQLSGGEQQRVALARAIAPRPRVMLMDEPFSGLDNRLRDGIRDETLEVLKDEGTAVLLVT 197

Query: 194 HEMGFARKVANRVIFMDEGKIVEDSPKDAFFDDPKSDRAKDFLAKI 239
           HE   A ++A+ +  M  GKIV+       ++ P    A  F + I
Sbjct: 198 HEPEEAMRMADNIALMRGGKIVQQGAPYNVYNSPVDKAAAAFFSDI 243


Lambda     K      H
   0.320    0.135    0.383 

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: 195
Number of extensions: 9
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: 241
Length of database: 362
Length adjustment: 26
Effective length of query: 215
Effective length of database: 336
Effective search space:    72240
Effective search space used:    72240
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: 48 (23.1 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