GapMind for catabolism of small carbon sources

 

Alignments for a candidate for actP in Dechlorosoma suillum PS

Align Acetate permease ActP-2/ActP2/ActP3 (characterized)
to candidate Dsui_0290 Dsui_0290 SSS sodium solute transporter

Query= TCDB::D5APM1
         (578 letters)



>FitnessBrowser__PS:Dsui_0290
          Length = 582

 Score =  808 bits (2088), Expect = 0.0
 Identities = 430/585 (73%), Positives = 479/585 (81%), Gaps = 21/585 (3%)

Query: 8   TRLAAVSALSLTPGLALAAGAIEGAVQKQPTNWTAIAMFGFFVVATLFITKWAAGRTKSA 67
           T   A++ L L      AA A+EG  +KQ TNWTAI MFG FV+ATL+ITKWAA +TK+A
Sbjct: 5   TNTLALAGLGLLSSPVFAA-ALEGQAEKQATNWTAIIMFGAFVLATLWITKWAASKTKTA 63

Query: 68  ADFYTAGGGITGFQNGLAIAGDYMSAASFLGISAAVMLQGYDGLIYSIGFLVGWPILTFL 127
           ADFYTAGGGITGFQNGLAIAGDYMSAASFLGISAAV   GYDGLIYSIGFLVGWPI+ FL
Sbjct: 64  ADFYTAGGGITGFQNGLAIAGDYMSAASFLGISAAVFANGYDGLIYSIGFLVGWPIIMFL 123

Query: 128 MAERLRNLGKFTFADVAAFPFAQTPVRVFAAMSTLVVVAFYLIAQMVGAGQLIKLLFGLE 187
           MAERLRNLGKFTFADVAA+ F  TP+R  AA  TLVVVAFYLIAQMVGAGQLIKLLFGL+
Sbjct: 124 MAERLRNLGKFTFADVAAYRFQATPIRALAASGTLVVVAFYLIAQMVGAGQLIKLLFGLD 183

Query: 188 YLYAVIVVGILMMVYVLFGGMTATTWVQIIKACLLLGGASFMALMVMVHYGFSLESLFAD 247
           Y  AV++VGILMMVYVLFGGMTATTWVQIIKA LLL GASFM  MV+  YGFS E+LFAD
Sbjct: 184 YWMAVVLVGILMMVYVLFGGMTATTWVQIIKAVLLLSGASFMVFMVLAKYGFSPEALFAD 243

Query: 248 SVKVKTDLAL-------------AAGKTPEEAAAA-GISIMGPGTFVKDPISAISFGMAL 293
           +V++KTDLA              A  +T   AAAA G SIMGPG+F+KDPISAISFGMAL
Sbjct: 244 AVRIKTDLAAKGLLAKALETDPSATAETVAAAAAAKGQSIMGPGSFIKDPISAISFGMAL 303

Query: 294 MFGTAGLPHILMRFFTVPSAKEARKSVMWATVWIGYFYMLTFIIGFGAIVYVLTNPGLVS 353
           MFGTAGLPHILMRFFTVP  KEARKSV WAT WIGYFY+LTFIIGFGAIV V TNP  + 
Sbjct: 304 MFGTAGLPHILMRFFTVPDGKEARKSVFWATTWIGYFYILTFIIGFGAIVLVGTNPEFL- 362

Query: 354 YDAKGALTLVGGNNMAAIHLAQAVGGNIFLGFISAVAFATILAVVAGLTLSGASAVSHDL 413
            DAKG L   GG NMAAIHLA AVGGN+FLGFISAVAFATILAVVAGLTLSGASAVSHDL
Sbjct: 363 -DAKGVLK--GGGNMAAIHLANAVGGNVFLGFISAVAFATILAVVAGLTLSGASAVSHDL 419

Query: 414 YSTVFKNGKADSASELRVSRITTICLGIVAVVLGLAFEKQNIAFMVSLAFAIAASANFPV 473
           Y++VF++G  DSA+E+RVS++TT+ LGI+AVVLG+AFEKQNIAFMVSLAFAIAASANFPV
Sbjct: 420 YASVFRHGNVDSATEMRVSKMTTVALGIIAVVLGIAFEKQNIAFMVSLAFAIAASANFPV 479

Query: 474 LFMSLLWKGMTTRGAVIGGSLGLISSVALTVISPSVWEATLGFEKGSAPFPYTSPALFSM 533
           LFMS+LWK  TT+GA  GG LGLI++V LTV+S S+W   LG    +  FPY SPALFSM
Sbjct: 480 LFMSVLWKDCTTKGAFYGGFLGLITAVVLTVLSKSIWVDILG--NKTEIFPYASPALFSM 537

Query: 534 VLGFAGIWLFSITDKSRRGDQDRDGYLAQEIRSETGIGAAEASAH 578
             GF GIWLFS+ D+S +  ++R  YL QEIRSETGIGAA AS+H
Sbjct: 538 AAGFIGIWLFSLMDRSEQAAKERVAYLDQEIRSETGIGAAAASSH 582


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: 1220
Number of extensions: 53
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: 582
Length adjustment: 36
Effective length of query: 542
Effective length of database: 546
Effective search space:   295932
Effective search space used:   295932
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 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