GapMind for catabolism of small carbon sources

 

Alignments for a candidate for potD in Pseudomonas simiae WCS417

Align Putrescine-binding periplasmic protein SpuD (characterized)
to candidate GFF5297 PS417_27120 ABC transporter substrate-binding protein

Query= SwissProt::Q02UB7
         (367 letters)



>FitnessBrowser__WCS417:GFF5297
          Length = 364

 Score =  421 bits (1083), Expect = e-122
 Identities = 198/338 (58%), Positives = 258/338 (76%), Gaps = 1/338 (0%)

Query: 30  LHVYNWSDYIAPDTLEKFTKETGIKVVYDVYDSNEVLEAKLLAGKSGYDVVVPSNSFLAK 89
           +H+YNWSDYI  DTL  F K +GIK VYDV+DSNE LE KLLAG++GYDVVVPSN FL K
Sbjct: 28  VHIYNWSDYIGTDTLANFEKASGIKPVYDVFDSNETLEGKLLAGRTGYDVVVPSNHFLGK 87

Query: 90  QIKAGVYQKLDKSKLPNWKNLNKDLMHTLEVSDPGNEHAIPYMWGTIGIGYNPDKVKAAF 149
           QIKAG +QKLDKS L N+ NL+  L+  LE +DPGN++A+PY+WGT GIGYN DK K   
Sbjct: 88  QIKAGAFQKLDKSLLTNYANLDPALLKRLEKNDPGNQYAVPYLWGTNGIGYNGDKGKEVL 147

Query: 150 GDNAPVDSWDLVFKPENIQKLKQCGVSFLDSPTEILPAALHYLGYKPDTDNPKELKAAEE 209
           G +  +DSW ++F+PEN++KL  CGVSF+DS  E+LPA L+Y+G  P++ NP + K AEE
Sbjct: 148 GVDH-IDSWAVLFEPENMKKLATCGVSFMDSADEMLPAVLNYMGLNPNSTNPDDYKKAEE 206

Query: 210 LFLKIRPYVTYFHSSKYISDLANGNICVAIGYSGDIYQAKSRAEEAKNKVTVKYNIPKEG 269
             LK+RPYVTYFHSSKYISDLANGNICVA G+SGD++QAK+RA EA   V + Y IPKEG
Sbjct: 207 KLLKVRPYVTYFHSSKYISDLANGNICVAAGFSGDVFQAKARAAEAGKGVNIAYTIPKEG 266

Query: 270 AGSFFDMVAIPKDAENTEGALAFVNFLMKPEIMAEITDVVQFPNGNAAATPLVSEAIRND 329
              +FD++AIPKDA N + A AF+N+L++PE++A+++D V + N N  A  L+ ++IR D
Sbjct: 267 GNLWFDVLAIPKDATNVKEAHAFINYLLQPEVIAQVSDYVGYANPNPGADKLMEQSIRTD 326

Query: 330 PGIYPSEEVMKKLYTFPDLPAKTQRAMTRSWTKIKSGK 367
             +YP + V+ + +   +LP K QR MTRSWTK+K+GK
Sbjct: 327 EAVYPPQAVLDRTFVNFELPPKVQRLMTRSWTKVKTGK 364


Lambda     K      H
   0.315    0.133    0.390 

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: 458
Number of extensions: 15
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: 367
Length of database: 364
Length adjustment: 30
Effective length of query: 337
Effective length of database: 334
Effective search space:   112558
Effective search space used:   112558
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 49 (23.5 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