Alignments for a candidate for actP in Cereibacter sphaeroides ATCC 17029

GapMind for catabolism of small carbon sources

Alignments for a candidate for actP in Cereibacter sphaeroides ATCC 17029

Align Acetate permease ActP-2/ActP2/ActP3 (characterized)
to candidate WP_011842723.1 RSPH17029_RS19600 cation acetate symporter

Query= TCDB::D5APM1
         (578 letters)



>NCBI__GCF_000015985.1:WP_011842723.1
          Length = 576

 Score =  888 bits (2294), Expect = 0.0
 Identities = 463/580 (79%), Positives = 508/580 (87%), Gaps = 6/580 (1%)

Query: 1   MSPVTTFTRLAAV-SALSLTPGLALAAGAIEGAVQKQPTNWTAIAMFGFFVVATLFITKW 59
           MS +T+  RLA V +AL L P LALAAG   G VQKQ TN+TAI MF  FVV TLFITKW
Sbjct: 1   MSRLTSSRRLAVVMAALILLPTLALAAGPDLGEVQKQATNYTAIGMFAAFVVFTLFITKW 60

Query: 60  AAGRTKSAADFYTAGGGITGFQNGLAIAGDYMSAASFLGISAAVMLQGYDGLIYSIGFLV 119
           AA +TKSAADFYTAGGGITGFQNGLAIAGDYMSAASFLGISAAVM  G+DGLIYSIGFLV
Sbjct: 61  AAAKTKSAADFYTAGGGITGFQNGLAIAGDYMSAASFLGISAAVMASGFDGLIYSIGFLV 120

Query: 120 GWPILTFLMAERLRNLGKFTFADVAAFPFAQTPVRVFAAMSTLVVVAFYLIAQMVGAGQL 179
           GWPILTFLMAERLRNLG+FTFADVAAF FAQTPVRVFAA STLVVVAFYLIAQMVGAGQL
Sbjct: 121 GWPILTFLMAERLRNLGQFTFADVAAFRFAQTPVRVFAASSTLVVVAFYLIAQMVGAGQL 180

Query: 180 IKLLFGLEYLYAVIVVGILMMVYVLFGGMTATTWVQIIKACLLLGGASFMALMVMVHYGF 239
           IKLLFGLEY  AV++VG LMM+YVLFGGMTATTWVQIIKACLLLGGA+FMA+MVM+ YGF
Sbjct: 181 IKLLFGLEYWVAVVIVGGLMMIYVLFGGMTATTWVQIIKACLLLGGATFMAVMVMMQYGF 240

Query: 240 SLESLFADSVKVKTDLAL-AAGKTPEEAAAAGISIMGPGTFVKDPISAISFGMALMFGTA 298
           SLE  FA +V+VK  +A    G TPE+AAAAG SIMGPG F+ DPISAISFGMALMFGTA
Sbjct: 241 SLERFFAAAVEVKAQIAAQTPGTTPEDAAAAGQSIMGPGKFITDPISAISFGMALMFGTA 300

Query: 299 GLPHILMRFFTVPSAKEARKSVMWATVWIGYFYMLTFIIGFGAIVYVLTNPGLVSYDAKG 358
           GLPHILMRFFTVP AKEARKSVMWAT WIGYFY+LTFIIGFGAI +VLTNPG +  D  G
Sbjct: 301 GLPHILMRFFTVPDAKEARKSVMWATTWIGYFYLLTFIIGFGAITFVLTNPGFL--DETG 358

Query: 359 ALTLVGGNNMAAIHLAQAVGGNIFLGFISAVAFATILAVVAGLTLSGASAVSHDLYSTVF 418
           A  LVGG+NMAAIHLA+AVGGN+FLGFISAVAFATILAVVAGLTL+GASAVSHD+Y+TV 
Sbjct: 359 A--LVGGSNMAAIHLAKAVGGNLFLGFISAVAFATILAVVAGLTLAGASAVSHDIYATVI 416

Query: 419 KNGKADSASELRVSRITTICLGIVAVVLGLAFEKQNIAFMVSLAFAIAASANFPVLFMSL 478
           K  KA SA+EL+VSR T + LG++AV LG+ FEKQNIAFMVSLAFAIAASANFPVLF+S+
Sbjct: 417 KKNKAGSAAELKVSRFTVLALGVLAVALGIVFEKQNIAFMVSLAFAIAASANFPVLFLSV 476

Query: 479 LWKGMTTRGAVIGGSLGLISSVALTVISPSVWEATLGFEKGSAPFPYTSPALFSMVLGFA 538
           LWKG TTRG VIGG +GL+ SV LTV+SPSVWEATLG++KGSAPFPYTSPALFSM  GF 
Sbjct: 477 LWKGCTTRGVVIGGFIGLVVSVVLTVLSPSVWEATLGYDKGSAPFPYTSPALFSMTAGFV 536

Query: 539 GIWLFSITDKSRRGDQDRDGYLAQEIRSETGIGAAEASAH 578
           GIWLFS  D+S RG QDR G++AQ++RSETGIGAA ASAH
Sbjct: 537 GIWLFSTLDRSLRGRQDRAGFVAQQVRSETGIGAAAASAH 576


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: 1251
Number of extensions: 47
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: 576
Length adjustment: 36
Effective length of query: 542
Effective length of database: 540
Effective search space:   292680
Effective search space used:   292680
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 10 2024. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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 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