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 GFF2636 PS417_13430 spermidine/putrescine ABC transporter substrate-binding protein

Query= SwissProt::Q02UB7
         (367 letters)



>FitnessBrowser__WCS417:GFF2636
          Length = 359

 Score =  442 bits (1138), Expect = e-129
 Identities = 210/350 (60%), Positives = 263/350 (75%), Gaps = 2/350 (0%)

Query: 18  VAGMAQAADNKVLHVYNWSDYIAPDTLEKFTKETGIKVVYDVYDSNEVLEAKLLAGKSGY 77
           VA + QAA+   + +YNWSDYIAPDT + F KETGI   YDVYDSNE L+ KL+ GKSGY
Sbjct: 12  VASIGQAAET--VKIYNWSDYIAPDTTKNFQKETGIGFTYDVYDSNETLDGKLMTGKSGY 69

Query: 78  DVVVPSNSFLAKQIKAGVYQKLDKSKLPNWKNLNKDLMHTLEVSDPGNEHAIPYMWGTIG 137
           DVV PSN F+A+QI+ G  +KLDKS+LPNWKNLN  L+  LE +DPGN H  PY+WG+ G
Sbjct: 70  DVVFPSNHFMARQIQGGALKKLDKSQLPNWKNLNPVLLKALENNDPGNAHGFPYLWGSTG 129

Query: 138 IGYNPDKVKAAFGDNAPVDSWDLVFKPENIQKLKQCGVSFLDSPTEILPAALHYLGYKPD 197
           IGYN DKVKA  GDNAPVDSWDL+FKPEN+ KL++CGV+ LD+  E+LPAAL+YLG    
Sbjct: 130 IGYNIDKVKAVLGDNAPVDSWDLIFKPENMAKLQKCGVAILDNGPELLPAALNYLGLPHH 189

Query: 198 TDNPKELKAAEELFLKIRPYVTYFHSSKYISDLANGNICVAIGYSGDIYQAKSRAEEAKN 257
           +  P++ K AE+L +K+RPYV YFHSSKY +DLANG+ICVA+G+SGDI QA+SRA+EAKN
Sbjct: 190 SKKPEDYKKAEDLLMKVRPYVAYFHSSKYTADLANGDICVAVGFSGDILQAESRAKEAKN 249

Query: 258 KVTVKYNIPKEGAGSFFDMVAIPKDAENTEGALAFVNFLMKPEIMAEITDVVQFPNGNAA 317
            V + YNIPKEGA  +FDMVA+P DA N     AF+N+L++P++MA IT+ V + NGN A
Sbjct: 250 GVNIGYNIPKEGAAIWFDMVAMPADAPNEAAGYAFMNYLLRPQVMASITNYVHYANGNQA 309

Query: 318 ATPLVSEAIRNDPGIYPSEEVMKKLYTFPDLPAKTQRAMTRSWTKIKSGK 367
           A  LV  AI+ D  IYPS E+M KL+    +P    R  TR W  I++GK
Sbjct: 310 ADSLVDPAIKADTKIYPSPEMMGKLFALEAMPLNIDRVRTRVWNTIRTGK 359


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: 482
Number of extensions: 13
Number of successful extensions: 1
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: 359
Length adjustment: 29
Effective length of query: 338
Effective length of database: 330
Effective search space:   111540
Effective search space used:   111540
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