Alignments for a candidate for ppa in Hydrogenophaga taeniospiralis CCUG 15921 NBRC 102512

GapMind for catabolism of small carbon sources

Alignments for a candidate for ppa in Hydrogenophaga taeniospiralis CCUG 15921 NBRC 102512

Align Phenylacetate permease, Ppa (characterized)
to candidate WP_068166475.1 HTA01S_RS00870 cation acetate symporter

Query= TCDB::O50471
         (520 letters)



>NCBI__GCF_001592305.1:WP_068166475.1
          Length = 575

 Score =  670 bits (1729), Expect = 0.0
 Identities = 337/536 (62%), Positives = 414/536 (77%), Gaps = 17/536 (3%)

Query: 2   NWTAISMFMVFVCFTLLVTRWAALRTRSASDFYTAGGGLTGMQNGLAIAGDMISAASFLG 61
           NWTAI MF +FV  TL +T+WAA +T+SASDFYTAGGG+TG QNGLAIAGD +SAASFLG
Sbjct: 40  NWTAIGMFALFVVGTLFITKWAAAKTKSASDFYTAGGGITGFQNGLAIAGDYMSAASFLG 99

Query: 62  ISAMMFMNGYDGLLYALGVLAGWPIILFLIAERLRNLGKYTFADVVSYRLAQTPVRLTSA 121
           ISA +  +G+DGL+Y++G L GWP+I FL+AERLRNLGK+TFADV ++R  QTP+R+ +A
Sbjct: 100 ISAAVMASGFDGLIYSIGFLVGWPVITFLMAERLRNLGKFTFADVAAFRFNQTPIRIFAA 159

Query: 122 FGTLVVALMYLVAQMVGAGKLIELLFGISYLYAVMLVGVLMVAYVTFGGMLATTWVQIIK 181
            GTLVV   YL+AQMVGAG+LI+LLFG+ Y  AV++VG LM+ YV FGGM ATTWVQIIK
Sbjct: 160 SGTLVVVAFYLIAQMVGAGQLIKLLFGLEYYIAVIIVGALMMVYVLFGGMTATTWVQIIK 219

Query: 182 AVMLLSGTSFMAFMVLKHFGFSTEAMFASAV---------------AVHAKGQAIMAPGG 226
           A +LL G +FMA  VL HFGFS EAMFASAV               A  A GQ+IM PG 
Sbjct: 220 ACLLLGGATFMALSVLWHFGFSPEAMFASAVQIKTDLALKDGKIAEAATAAGQSIMGPGN 279

Query: 227 LLSNPVDAISLGLGMMFGTAGLPHILMRFFTVSDAKEARKSVFYATGFIGYFYLLLIVIG 286
            + +P+ AIS G+ +MFGTAGLPHILMRFFTV  AKEARKSV +ATG+IGYFYLL  +IG
Sbjct: 280 FVKDPISAISFGMALMFGTAGLPHILMRFFTVPSAKEARKSVMWATGWIGYFYLLTFIIG 339

Query: 287 FGAIVMVGTEPSYRDATGAIIGGGNMIAVHLAQAVGGNLFLGFISAVAFATILAVVAGLA 346
           FGAI  V   P + DA G ++GG NM AVHLA AVGGN+FLGFISAVAFATILAVVAGL 
Sbjct: 340 FGAITFVLINPQFLDAKGGLLGGNNMAAVHLANAVGGNVFLGFISAVAFATILAVVAGLT 399

Query: 347 LSGASAVSHDLYACVIRQGKATEQEEMRVSRIATLLIGLLAVLLGLMFESQNIAFLSGLV 406
           LSGASAVSHDLYA VI++G+A    E+RVS+  T+ +G++AV+LG+ FE QNIAF+  L 
Sbjct: 400 LSGASAVSHDLYATVIKKGQADSASELRVSKATTIALGIIAVVLGIAFEKQNIAFMVSLA 459

Query: 407 LAVAASVNFPVLLLSMFWKGLTTRGAVCGSMAGLASAVLLVVLGPAVWVNVLHHEK--AL 464
            A+AAS NFPVL +S+ WK  TT+GAV G   GL S+V+L V+ P+VW   L + K  AL
Sbjct: 460 FAIAASANFPVLFMSVLWKDCTTKGAVIGGFLGLISSVVLTVVSPSVWEVTLGNPKGSAL 519

Query: 465 FPYSNPALFSMSLAFLSAWVFSVTDSSERASEERGRYLAQFIRSMTGIGAAGASKH 520
           FPY++PALFSM++ F+  W+FS+ D+S+RA  +RG +LAQ +RS TGIGA+GAS H
Sbjct: 520 FPYTSPALFSMTIGFVGIWLFSILDNSQRAKVDRGGFLAQQVRSETGIGASGASGH 575


Lambda     K      H
   0.328    0.139    0.407 

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: 927
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: 520
Length of database: 575
Length adjustment: 36
Effective length of query: 484
Effective length of database: 539
Effective search space:   260876
Effective search space used:   260876
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 (21.8 bits)
S2: 52 (24.6 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