Alignments for a candidate for actP in Sulfuricurvum kujiense DSM 16994

GapMind for catabolism of small carbon sources

Alignments for a candidate for actP in Sulfuricurvum kujiense DSM 16994

Align Acetate permease; SubName: Full=Actetate permease; SubName: Full=Cation acetate symporter; SubName: Full=Cation/acetate symporter (characterized, see rationale)
to candidate WP_013460689.1 SULKU_RS09190 cation acetate symporter

Query= uniprot:A0A1N7U9G2
         (552 letters)



>NCBI__GCF_000183725.1:WP_013460689.1
          Length = 552

 Score =  786 bits (2029), Expect = 0.0
 Identities = 393/548 (71%), Positives = 471/548 (85%), Gaps = 9/548 (1%)

Query: 12  SIFAPAVWAADALTGEVHKQPLNVSAIVMFVVFVGATLCITYWASKRNKSAADYYAAGGK 71
           ++F+ A +A +AL+G V KQPLN+SAI+MF++FVGATL ITYWA+KR K+A D+Y AGG 
Sbjct: 7   ALFSVAAFAGEALSGAVEKQPLNMSAIIMFLIFVGATLGITYWAAKRTKTAKDFYTAGGG 66

Query: 72  ITGFQNGLAIAGDYMSAASFLGISALVYTSGYDGLIYSIGFLVGWPIILFLIAERLRNLG 131
           ITGFQNG+AIAGDYMSAASFLGISALVY  GYDGLIYSIGFLVGWPIILF++AE+LRNLG
Sbjct: 67  ITGFQNGMAIAGDYMSAASFLGISALVYAKGYDGLIYSIGFLVGWPIILFMVAEQLRNLG 126

Query: 132 KYTFADVASYRLGQTQIRSLSACGSLVVVAFYLIAQMVGAGKLIQLLFGLDYHVAVILVG 191
           KYTFADVASYRL QT IR+L+A GS++ V  YLIAQMVGAGKLIQLLFGLDY +AVILVG
Sbjct: 127 KYTFADVASYRLRQTPIRTLAAFGSILTVVLYLIAQMVGAGKLIQLLFGLDYEIAVILVG 186

Query: 192 ILMVLYVLFGGMLATTWVQIIKAVLLLSGASFMALMVMKHVNFDFNALFSEAIKVHPKGE 251
           +LM+LYV FGGMLATTWVQIIKA LLLSGA+FMA+ VM H NF+F +LF+ A+ +  K +
Sbjct: 187 VLMILYVTFGGMLATTWVQIIKAFLLLSGATFMAVAVMAHYNFNFESLFATAVSM--KDQ 244

Query: 252 AIMSPGGLVKDPISAFSLGLALMFGTAGLPHILMRFFTVSDAKEARKSVFYATGFIGYFY 311
           +IM+PG LV DPISA SLG+ALMFGTAGLPHILMRFFTVSDAKEARKSVFYATGFIGYFY
Sbjct: 245 SIMAPGKLVSDPISAISLGIALMFGTAGLPHILMRFFTVSDAKEARKSVFYATGFIGYFY 304

Query: 312 ILTFIIGFGAILLVSTNPAFKDAA-------GALMGGNNMAAVHLANAVGGSIFLGFISA 364
           ILTFIIGFGAI++V  NP + D A         ++GG+NMAA+HL++AVGG  FLGF+SA
Sbjct: 305 ILTFIIGFGAIVMVFQNPQYLDLAKQAVDGGAPILGGDNMAAIHLSHAVGGDFFLGFMSA 364

Query: 365 VAFATILAVVAGLTLAGASAVSHDLYASVIKKGKANDKDEIRVSKITTIALGVLAIGLGI 424
           VAFATILAVV+GLTLAGASA+SHDLYASV++ G+A+   E++VSKI+T+ LG++AI LGI
Sbjct: 365 VAFATILAVVSGLTLAGASAISHDLYASVLRAGRADGMMEMKVSKISTVVLGIVAIYLGI 424

Query: 425 LFESQNIAFMVGLAFSIAASCNFPVLLLSMYWKNLTTRGAMIGGWLGLVSAVGLMVLGPT 484
            FE QNIAFMVGLAF+IAAS NFP+L LSM+W  LTTRGA++GG LGL++A  L+VLGPT
Sbjct: 425 AFEDQNIAFMVGLAFAIAASANFPILFLSMFWSKLTTRGALLGGSLGLLTAGVLVVLGPT 484

Query: 485 IWVSILHHEKAIFPYEYPALFSMIIAFVGIWFFSITDKSSAAEKERALYFPQFVRSQTGL 544
           +WV +L + +AIFPY+YPALFS+  AF+GIWFFSITDKS  +EKE+  Y  Q++RSQTG+
Sbjct: 485 VWVDVLKNAEAIFPYKYPALFSVSAAFIGIWFFSITDKSENSEKEKEAYEAQYIRSQTGI 544

Query: 545 GSSGAVSH 552
           G+ GAV H
Sbjct: 545 GAEGAVEH 552


Lambda     K      H
   0.327    0.140    0.415 

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: 1066
Number of extensions: 55
Number of successful extensions: 3
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: 552
Length of database: 552
Length adjustment: 36
Effective length of query: 516
Effective length of database: 516
Effective search space:   266256
Effective search space used:   266256
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: 53 (25.0 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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