Alignments for a candidate for actP in Trichlorobacter lovleyi SZ

GapMind for catabolism of small carbon sources

Alignments for a candidate for actP in Trichlorobacter lovleyi SZ

Align Acetate permease ActP-2/ActP2/ActP3 (characterized)
to candidate WP_012469463.1 GLOV_RS06890 cation acetate symporter

Query= TCDB::D5APM1
         (578 letters)



>NCBI__GCF_000020385.1:WP_012469463.1
          Length = 665

 Score =  444 bits (1141), Expect = e-129
 Identities = 266/642 (41%), Positives = 375/642 (58%), Gaps = 82/642 (12%)

Query: 2   SPVTTFTRLAAVSALSLTPGLALAAGAIEGAVQKQPTNWTAIAMFGFFVVATLFITKWAA 61
           +P  T    A  +  +  P  A    A  G ++  P     I +F   + AT+ +  W+A
Sbjct: 41  APAATVAPAADAAKQAAAPAPAPVKDAKAG-LKANPV--VTIPIFLLIIGATMAVVVWSA 97

Query: 62  GRTKSAADFYTAGGGITGFQNGLAIAGDYMSAASFLGISAAVMLQGYDGLIYSIGFLVGW 121
            +TKSAADFYTAGGGITG QNG AIAGDYMSAASFLGIS  + L GYDG +YS+G+LV +
Sbjct: 98  KKTKSAADFYTAGGGITGTQNGWAIAGDYMSAASFLGISGMISLYGYDGFMYSVGWLVAY 157

Query: 122 PILTFLMAERLRNLGKFTFADVAAFPFAQTPVRVFAAMSTLVVVAFYLIAQMVGAGQLIK 181
             +  ++AE  RN GK+T  D+ +F  +  PVR  AA+ST+ V  FYL AQMVGAG+L++
Sbjct: 158 ITVLLIVAEPCRNAGKYTLGDILSFRTSPKPVRAVAAISTVSVSTFYLTAQMVGAGKLMQ 217

Query: 182 LLFGLEYLYAVIVVGILMMVYVLFGGMTATTWVQIIKACLLLGGASFMALMVMVHYGFSL 241
           LL G+ Y  A+I VGILM+ YV+FGGMTATTWVQIIKA LL+ GA+ +++MV +  GF+ 
Sbjct: 218 LLLGVPYKTAIIGVGILMVGYVVFGGMTATTWVQIIKAGLLMTGAALLSIMVSIKSGFNP 277

Query: 242 ESLFADSVKVKT--------DLALAAGKTPEEAAAAGISIMGPGTFVKDPISAISFGMAL 293
              F+D    +          + L   K       AG   + PG F+ +P+  IS GMAL
Sbjct: 278 FQFFSDIATSQNIIDHVKLLPIYLKEVKAGTATMDAGQRFLEPGLFLTNPLDQISLGMAL 337

Query: 294 MFGTAGLPHILMRFFTVPSAKEARKSVMWATVWIGYFYMLTFIIGFGAIVYVLTNPGLVS 353
           + GTAG+PHILMRFFTVP+A+ ARKSV+ A   IG FY+LT ++GFGA ++V T  G+ S
Sbjct: 338 VLGTAGMPHILMRFFTVPTAQAARKSVIVAMFIIGSFYILTTLLGFGAAIHV-TPQGIKS 396

Query: 354 YDAKGALTLVGGNNMAAIHLAQAVG-------GNIFLGFISAVAFATILAVVAGLTLSGA 406
            DA        G NMAA+ LA+ +G       G++ L F+ AVAFATILAVV+GL L+ +
Sbjct: 397 VDA--------GGNMAAMMLAKQLGSEFSPFIGDLLLAFLCAVAFATILAVVSGLVLAAS 448

Query: 407 SAVSHDLYSTVFKNGKADSASELRVSRITTICLGIVAVVLGLAFEKQNIAFMVSLAFAIA 466
           +A++HD+Y  V K+G AD + ++  +R T+  +G V +++G+A EKQN+A +V+LAFA+A
Sbjct: 449 AAIAHDIYVNVIKDGHADQSEQVFAARTTSFIVGAVGIIIGIAAEKQNVAHLVALAFAVA 508

Query: 467 ASANFPVLFMSLLWKGMTTRGAVIGGSLGLISSVALTVISPSV----------------- 509
           +S N PV+ MSL WK   T G + G  +G ++S+ L +ISP++                 
Sbjct: 509 SSGNLPVVVMSLFWKKFNTAGVIAGLVVGTVASIGLVMISPNMTYPEVVANNAKLAYSKL 568

Query: 510 ---------------------------------WEATLGFEKGSAPFPYTSPALFSMVLG 536
                                             ++ LG EK    F   +P + S+ LG
Sbjct: 569 EKEIADGKVKPEAMEKTLKTIETKKAEEAKNRGGKSMLGLEK--PLFTLKNPGIVSIPLG 626

Query: 537 FAGIWLFSITDKSRRGDQDRDGYLAQEIRSETGIGAAEASAH 578
           F    L ++   S++ ++  D      +R  TG+G A+A  H
Sbjct: 627 FIAAILATLAFPSKKAEEMWDEIY---VRQNTGLGMAKAVDH 665


Lambda     K      H
   0.326    0.138    0.405 

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: 1068
Number of extensions: 66
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: 578
Length of database: 665
Length adjustment: 37
Effective length of query: 541
Effective length of database: 628
Effective search space:   339748
Effective search space used:   339748
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Apr 09 2024. 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources