GapMind for catabolism of small carbon sources

 

Alignments for a candidate for putP in Pseudomonas litoralis 2SM5

Align High-affinity proline transporter PutP (characterized)
to candidate WP_090274945.1 BLU11_RS15570 sodium/proline symporter PutP

Query= SwissProt::P94392
         (473 letters)



>NCBI__GCF_900105005.1:WP_090274945.1
          Length = 500

 Score =  526 bits (1355), Expect = e-154
 Identities = 262/468 (55%), Positives = 344/468 (73%), Gaps = 13/468 (2%)

Query: 1   MLLIGYFAYKRTSNLTDYMLGGRSLGPAVTALSAGAADMSGWLLMGLPGAMFSTGLSGAW 60
           ML IGY+AY++T++L DYML GR L P V ALSAGA+DMSGWLLMGLPGA++++GL  AW
Sbjct: 18  MLGIGYYAYRQTTDLDDYMLAGRKLSPGVAALSAGASDMSGWLLMGLPGAIYASGLVEAW 77

Query: 61  IVIGLCLGAWANWLYVAPRLRTYTEKAGNSITIPGFLENRFGDQTKLLRLFSGIVILVFF 120
           I IGL +GA+ NW +VAPRLR+YTE + NSIT+P F+ENRF D+T+LLR+ SG++ILVFF
Sbjct: 78  IAIGLTIGAYLNWRFVAPRLRSYTEVSNNSITVPSFMENRFKDKTRLLRIASGVIILVFF 137

Query: 121 TFYVSSGMVSGGVLFNSILGMDYHTGLWIVTGVVVAYTLFGGFLAVSWTDFVQGIIMFAA 180
           TFYVSSGMV+GGV F +     Y  G+ +V+G+ + YTLFGGFL  S TD VQG++M AA
Sbjct: 138 TFYVSSGMVAGGVFFEASFNTPYLFGMLLVSGITLTYTLFGGFLGASLTDVVQGLLMLAA 197

Query: 181 LILVPIVTFFHTGGAGDTVAEIRSVDP-----------DMFNIFKGTSVLGIISLFAWGL 229
           LI+VP++T    GG G+T+  I + D               ++  G S+L IIS  +WGL
Sbjct: 198 LIIVPVLTVIGMGGLGETIDAIHAADAAHNLANPGDELHRTSLLFGGSLLAIISAASWGL 257

Query: 230 GYFGQPHIIVRFMAITSVKEIKRARRIGMGWMILSAVGAVLTGLGGIAYYHQRGMTLKDP 289
           GYFGQPHIIVRFMA+ S  + K  RRIG+GWMIL A GAV TGL G+ Y+H     L +P
Sbjct: 258 GYFGQPHIIVRFMALRSSADAKAGRRIGIGWMILVASGAVFTGLIGVGYFHTSNEVLDNP 317

Query: 290 ETIFIQLGNILFHPIITGFLISAILAAIMSTISSQLLVTSSSLVEDLYKSMFRRSASDKE 349
           ET+F+ L  ILFHP++ G +++A+LAAIMST+SSQL+V SS+LVEDLYK +F +  +  +
Sbjct: 318 ETVFLLLSQILFHPLVAGLVLAAVLAAIMSTVSSQLIVCSSALVEDLYK-IFGKDLTALQ 376

Query: 350 LVFLGRLAVLAVSIVALVLAWEKNNTILGLVSYAWAGFGASFGPVVLLSLFWKRMTKWGA 409
            V LGRL VL V+++A +LA +  + ILGLV++AWAGFGA+FGP++LLSLFW+++T  GA
Sbjct: 377 QVRLGRLGVLTVAVIAALLAIDPRSNILGLVAFAWAGFGAAFGPIILLSLFWRKLTAMGA 436

Query: 410 LAGMIVGAATVIIWAN-AGLSDFLYEMIPGFAASLLSVFFVSILTQAP 456
           LAGMI GA  V IW N A L   +YE++PGF A  +    VS+L + P
Sbjct: 437 LAGMITGAVVVGIWGNIASLQALMYEIVPGFLACTVVAIVVSLLIKTP 484


Lambda     K      H
   0.327    0.141    0.432 

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: 808
Number of extensions: 41
Number of successful extensions: 4
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: 473
Length of database: 500
Length adjustment: 34
Effective length of query: 439
Effective length of database: 466
Effective search space:   204574
Effective search space used:   204574
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: 52 (24.6 bits)

This GapMind analysis is from Sep 24 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