GapMind for catabolism of small carbon sources

 

Aligments for a candidate for glt in Pseudomonas fluorescens FW300-N2E2

Align Proton/glutamate-aspartate symporter; Glutamate-aspartate carrier protein; Proton-glutamate-aspartate transport protein (characterized)
to candidate Pf6N2E2_4148 Glutamate-aspartate carrier protein

Query= SwissProt::P21345
         (437 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4148 Glutamate-aspartate
           carrier protein
          Length = 443

 Score =  613 bits (1581), Expect = e-180
 Identities = 315/423 (74%), Positives = 369/423 (87%), Gaps = 1/423 (0%)

Query: 1   MKNIKFSLAWQILFAMVLGILLGSYLHYHSDSRDWLVVNLLSPAGDIFIHLIKMIVVPIV 60
           MK  + SLAWQIL  +VLGI LG+ L++ S  + W + N+L PAGDIFI LIKMIV+PIV
Sbjct: 1   MKKARLSLAWQILIGLVLGIALGALLNHFSAEKAWWISNVLQPAGDIFIRLIKMIVIPIV 60

Query: 61  ISTLVVGIAGVGDAKQLGRIGAKTIIYFEVITTVAIILGITLANVFQPGAGVDMSQLATV 120
           IS+L+VGIAGVGDAK+LGRIG KTI+YFEV+TT+AI++G+ LAN FQPG+G+DMS L TV
Sbjct: 61  ISSLIVGIAGVGDAKKLGRIGLKTILYFEVVTTIAIVVGLLLANFFQPGSGIDMSTLGTV 120

Query: 121 DISKYQSTTEAVQSSSHGIMGTILSLVPTNIVASMAKGEMLPIIFFSVLFGLGLSSLPAT 180
           DISKYQ+T   VQ   H  + TIL+L+P+NI A++A+GEMLPIIFFSVLFGLGLSSL + 
Sbjct: 121 DISKYQATAAEVQHE-HAFIQTILNLIPSNIFAAVARGEMLPIIFFSVLFGLGLSSLQSD 179

Query: 181 HREPLVTVFRSISETMFKVTHMVMRYAPVGVFALIAVTVANFGFSSLWPLAKLVLLVHFA 240
            R+PLV +F+ +SE+MFKVTHM+M+YAP+GVFALIAVTVANFGF+SL PLAKLV+LV+ A
Sbjct: 180 LRDPLVKMFQGVSESMFKVTHMIMQYAPIGVFALIAVTVANFGFASLLPLAKLVILVYVA 239

Query: 241 ILFFALVVLGIVARLCGLSVWILIRILKDELILAYSTASSESVLPRIIEKMEAYGAPVSI 300
           I FFA VVLG++ARL G SV  L+RI KDEL+LAYSTASSE+VLPR+IEKMEAYGAP +I
Sbjct: 240 IAFFAFVVLGVIARLFGFSVLKLMRIFKDELVLAYSTASSETVLPRVIEKMEAYGAPKAI 299

Query: 301 TSFVVPTGYSFNLDGSTLYQSIAAIFIAQLYGIDLSIWQEIILVLTLMVTSKGIAGVPGV 360
            SFVVPTGYSFNLDGSTLYQSIAAIFIAQLYGIDLSI Q+++LVLTLMVTSKGIAGVPGV
Sbjct: 300 CSFVVPTGYSFNLDGSTLYQSIAAIFIAQLYGIDLSISQQLLLVLTLMVTSKGIAGVPGV 359

Query: 361 SFVVLLATLGSVGIPLEGLAFIAGVDRILDMARTALNVVGNALAVLVIAKWEHKFDRKKA 420
           SFVVLLATLGSVGIPLEGLAFIAGVDRI+DMARTALNV+GNALAVLVIA+WE  +D  K 
Sbjct: 360 SFVVLLATLGSVGIPLEGLAFIAGVDRIMDMARTALNVIGNALAVLVIARWEGMYDDAKG 419

Query: 421 LAY 423
             Y
Sbjct: 420 QRY 422


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: 645
Number of extensions: 16
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: 437
Length of database: 443
Length adjustment: 32
Effective length of query: 405
Effective length of database: 411
Effective search space:   166455
Effective search space used:   166455
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 preprint 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