GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gltP in Pseudomonas fluorescens GW456-L13

Align Proton/glutamate-aspartate symporter; Glutamate-aspartate carrier protein; Proton-glutamate-aspartate transport protein (characterized)
to candidate PfGW456L13_2016 Aerobic C4-dicarboxylate transporter for fumarate, L-malate, D-malate, succunate, aspartate

Query= SwissProt::P21345
         (437 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2016
          Length = 444

 Score =  321 bits (823), Expect = 3e-92
 Identities = 169/411 (41%), Positives = 266/411 (64%), Gaps = 13/411 (3%)

Query: 7   SLAWQILFAMVLGILLGSYLHYHSDSRDWLVVNLLSPAGDIFIHLIKMIVVPIVISTLVV 66
           SL +Q++ A+ +GILLG   H++  +        L P GD FI LIKM++ PI+  T+V 
Sbjct: 10  SLYFQVIVAIAIGILLG---HFYPQTGV-----ALKPLGDGFIKLIKMVIAPIIFCTVVS 61

Query: 67  GIAGVGDAKQLGRIGAKTIIYFEVITTVAIILGITLANVFQPGAGVDMSQLATVDISKYQ 126
           GIAG+ + K +G+ G   ++YFE+++T+A+++G+ + NV QPGAG+ +  ++T+D SK  
Sbjct: 62  GIAGMQNMKSVGKTGGYALLYFEIVSTLALLIGLVVVNVVQPGAGMHID-VSTLDTSKIA 120

Query: 127 STTEAVQSSSHGIMGTILSLVPTNIVASMAKGEMLPIIFFSVLFGLGLSSLPATHREPLV 186
               A +  S  I+  +L+++P  IV + A G++L ++ FSV+FG  L  L A + +P++
Sbjct: 121 GFISAGKDQS--IIAFVLNVIPNTIVGAFANGDILQVLMFSVIFGFALHRLGA-YGKPVL 177

Query: 187 TVFRSISETMFKVTHMVMRYAPVGVFALIAVTVANFGFSSLWPLAKLVLLVHFAILFFAL 246
                 +  MF + +M+M+ APVG F  +A T+  +G  SL  L +L++  +   + F L
Sbjct: 178 DFIDRFAHVMFNIINMIMKLAPVGAFGAMAFTIGAYGVGSLVQLGQLMICFYITCILFVL 237

Query: 247 VVLGIVARLCGLSVWILIRILKDELILAYSTASSESVLPRIIEKMEAYGAPVSITSFVVP 306
           +VLG + R  G SV  LIR +++EL++   T+SSES LPR++ K+E  GA  S+   V+P
Sbjct: 238 LVLGAICRAHGFSVIKLIRYIREELLIVLGTSSSESALPRMLIKLERLGAQKSVVGLVIP 297

Query: 307 TGYSFNLDGSTLYQSIAAIFIAQLYGIDLSIWQEIILVLTLMVTSKGIAGVPGVSFVVLL 366
           TGYSFNLDG+++Y ++AA+FIAQ     + +  +I L+L L+++SKG AGV G  F+VL 
Sbjct: 298 TGYSFNLDGTSIYLTMAAVFIAQATDTPMDLTAQITLLLVLLLSSKGAAGVTGSGFIVLA 357

Query: 367 ATLGSVG-IPLEGLAFIAGVDRILDMARTALNVVGNALAVLVIAKWEHKFD 416
           ATL +VG +P+ GLA I G+DR +  AR   N+VGNA+A LV+AKW  + D
Sbjct: 358 ATLSAVGHLPVAGLALILGIDRFMSEARALTNLVGNAVATLVVAKWVKELD 408


Lambda     K      H
   0.326    0.141    0.403 

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: 488
Number of extensions: 24
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: 437
Length of database: 444
Length adjustment: 32
Effective length of query: 405
Effective length of database: 412
Effective search space:   166860
Effective search space used:   166860
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 (21.7 bits)
S2: 51 (24.3 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