GapMind for catabolism of small carbon sources

 

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

Align PotG aka B0855, component of Putrescine porter (characterized)
to candidate Pf1N1B4_2538 Putrescine transport ATP-binding protein PotA (TC 3.A.1.11.1)

Query= TCDB::P31134
         (377 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2538 Putrescine transport
           ATP-binding protein PotA (TC 3.A.1.11.1)
          Length = 374

 Score =  264 bits (675), Expect = 3e-75
 Identities = 151/323 (46%), Positives = 207/323 (64%), Gaps = 13/323 (4%)

Query: 19  LLEIRNLTKSYDGQHA-VDDVSLTIYKGEIFALLGASGCGKSTLLRMLAGFEQPSAGQIM 77
           L+  R + KSYDG++  V D++L I KGE   LLG SG GK+T L MLAGFE P+AG+I 
Sbjct: 14  LVSFRGVQKSYDGENLIVKDLNLDIRKGEFLTLLGPSGSGKTTSLMMLAGFETPTAGEIQ 73

Query: 78  LDGVDLSQVPPYLRPINMMFQSYALFPHMTVEQNIAFGLKQDKLPKAEIASRVNEMLGLV 137
           L G  ++ VPP+ R I M+FQ+YALFPHMTV +N+AF L    L K +++ RV  +L +V
Sbjct: 74  LAGRSINNVPPHKRDIGMVFQNYALFPHMTVAENLAFPLTVRGLNKNDVSDRVKRVLSMV 133

Query: 138 HMQEFAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRDRMQLEVVDILE 197
            +  FA+R P QLSGGQ+QRVALAR+L   P+L+L+DEP+GALDK+LR+ MQ+E+  + +
Sbjct: 134 QLDTFAQRYPAQLSGGQQQRVALARALVFEPQLVLMDEPLGALDKQLREHMQMEIKHLHQ 193

Query: 198 RVGVTCVMVTHDQEEAMTMAGRIAIMNRGKFVQIGEPEEIYEHPTTRYSAEFIGSVNVFE 257
           R+GVT V VTHDQ EA+TM+ R+A+ ++G+  QI  P  +YE P   + A FIG  N   
Sbjct: 194 RLGVTVVYVTHDQGEALTMSDRVAVFHQGEIQQIAPPRSLYEEPKNTFVANFIGENNRLN 253

Query: 258 GVLKERQEDGLVLDSPGLVHPLKVDADASVVDNV--PVHVALRPEKIMLCEEPPANGC-N 314
           G L     D  V++   L    KV+A A  V     PV +++RPE++ L     +  C N
Sbjct: 254 GRLHSHTGDRCVVE---LGRGEKVEALAVNVGKTGEPVTLSIRPERVSL--NGSSESCVN 308

Query: 315 FAVGEVIHIAYLGDLSVYHVRLK 337
              G V    YLGD    HVR++
Sbjct: 309 RFSGRVAEFIYLGD----HVRVR 327


Lambda     K      H
   0.321    0.137    0.400 

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: 378
Number of extensions: 14
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: 377
Length of database: 374
Length adjustment: 30
Effective length of query: 347
Effective length of database: 344
Effective search space:   119368
Effective search space used:   119368
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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