GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gltP in Pseudomonas fluorescens FW300-N1B4

Align Proton/glutamate-aspartate symporter; Glutamate-aspartate carrier protein; Proton-glutamate-aspartate transport protein (characterized)
to candidate Pf1N1B4_4464 C4-dicarboxylate transport protein

Query= SwissProt::P21345
         (437 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4464 C4-dicarboxylate
           transport protein
          Length = 439

 Score =  317 bits (811), Expect = 6e-91
 Identities = 168/424 (39%), Positives = 270/424 (63%), Gaps = 18/424 (4%)

Query: 1   MKNIKFSLAWQILFAMVLGILLGSYLHYHSDSRDWLVVNLLSPAGDIFIHLIKMIVVPIV 60
           MK +K SL +QIL A++LG+++G +    + +        L P GD FI LIKM++ P+V
Sbjct: 5   MKVVK-SLYFQILCAVLLGVVVGHFWAQQAIA--------LKPLGDAFIKLIKMMIAPVV 55

Query: 61  ISTLVVGIAGVGDAKQLGRIGAKTIIYFEVITTVAIILGITLANVFQPGAG--VDMSQLA 118
             T+V GIAG+ D + LGR+ +KT++ F  +T +++ +G+    VF+PGAG  +D S L+
Sbjct: 56  FCTIVTGIAGMNDKRSLGRLLSKTMLLFLGLTVISLFIGLVAVYVFKPGAGMNIDPSHLS 115

Query: 119 TVDISKYQSTTEAVQSSSHGIMGTILSLVPTNIVASMAKGEMLPIIFFSVLFGLGLSSLP 178
           T  +S+Y  +   +     G++   + ++P   + + +KGE+LP++F +VL G  LSSL 
Sbjct: 116 TAGLSQYTESAAKL-----GVVEFFMHIIPDTFIGAFSKGEVLPVLFIAVLCGFALSSL- 169

Query: 179 ATHREPLVTVFRSISETMFKVTHMVMRYAPVGVFALIAVTVANFGFSSLWPLAKLVLLVH 238
               +P++ V  + S+ +FK+   +MR+AP+G F  +A TV  +G +SL  LAKL++ ++
Sbjct: 170 GDRGKPVLDVLEAASQMVFKIFSYLMRFAPIGAFGALAFTVGQYGITSLGSLAKLIMTLY 229

Query: 239 FAILFFALVVLGIVARLCGLSVWILIRILKDELILAYSTASSESVLPRIIEKMEAYGAPV 298
            A  FF  VVLG + R  G S+W L+R L++E ++   T+S+E V+PR++EK++A G   
Sbjct: 230 VACAFFVFVVLGSICRAHGFSLWKLLRYLREEFLVVLGTSSTEPVMPRMLEKLQALGCSK 289

Query: 299 SITSFVVPTGYSFNLDGSTLYQSIAAIFIAQLYGIDLSIWQEIILVLTLMVTSKGIAGVP 358
            +   V+PTGYSFNLDG+ +Y S+AAIFIAQ   IDL++ Q + ++  ++++SKG AGV 
Sbjct: 290 GVVGLVLPTGYSFNLDGTAIYLSLAAIFIAQACNIDLTVTQTLTMLAIMLLSSKGAAGVT 349

Query: 359 GVSFVVLLATLGSV-GIPLEGLAFIAGVDRILDMARTALNVVGNALAVLVIAKWEHKFDR 417
           G  FV L +TL  +  IPL GLA + G+DR +  AR   ++  NA+A +VI+  E+  DR
Sbjct: 350 GSGFVALASTLTVIHDIPLAGLALLIGIDRFMSEARALTSLASNAVATVVISISENACDR 409

Query: 418 KKAL 421
           +  L
Sbjct: 410 QVLL 413


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: 473
Number of extensions: 20
Number of successful extensions: 5
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: 439
Length adjustment: 32
Effective length of query: 405
Effective length of database: 407
Effective search space:   164835
Effective search space used:   164835
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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