GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glt in Pseudomonas fluorescens FW300-N2E3

Align Proton/glutamate-aspartate symporter; Glutamate-aspartate carrier protein; Proton-glutamate-aspartate transport protein (characterized)
to candidate AO353_10990 AO353_10990 glutamate:protein symporter

Query= SwissProt::P21345
         (437 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_10990
          Length = 443

 Score =  614 bits (1584), Expect = e-180
 Identities = 316/423 (74%), Positives = 368/423 (86%), Gaps = 1/423 (0%)

Query: 1   MKNIKFSLAWQILFAMVLGILLGSYLHYHSDSRDWLVVNLLSPAGDIFIHLIKMIVVPIV 60
           MK  K SLAWQIL  +VLGI +G+ L++ S  + W + N+L PAGDIFI LIKMIV+PIV
Sbjct: 1   MKKAKLSLAWQILIGLVLGIAIGALLNHFSAEKAWWISNVLQPAGDIFIRLIKMIVIPIV 60

Query: 61  ISTLVVGIAGVGDAKQLGRIGAKTIIYFEVITTVAIILGITLANVFQPGAGVDMSQLATV 120
           IS+LVVGIAGVGDAK+LGRIG KTIIYFE++TT+AI++G+ LANVF PG+G+DMS L TV
Sbjct: 61  ISSLVVGIAGVGDAKKLGRIGLKTIIYFEIVTTIAILVGLVLANVFHPGSGIDMSTLGTV 120

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

Query: 181 HREPLVTVFRSISETMFKVTHMVMRYAPVGVFALIAVTVANFGFSSLWPLAKLVLLVHFA 240
            REPLV +F+ +SE+MFKVTHM+M YAP+GVFALIAVTVANFGF+SL PLAKLV+LV+ A
Sbjct: 180 LREPLVKMFQGVSESMFKVTHMIMNYAPIGVFALIAVTVANFGFASLLPLAKLVILVYVA 239

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

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

Query: 361 SFVVLLATLGSVGIPLEGLAFIAGVDRILDMARTALNVVGNALAVLVIAKWEHKFDRKKA 420
           SFVVLLATLGSVGIPLEGLAFIAGVDRI+DMARTALNV+GNALAVLV+++WE  +D  K 
Sbjct: 360 SFVVLLATLGSVGIPLEGLAFIAGVDRIMDMARTALNVIGNALAVLVVSRWEGMYDDAKG 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: 641
Number of extensions: 21
Number of successful extensions: 2
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:

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