Alignments for a candidate for actP in Chlorobium limicola DSM 245

GapMind for catabolism of small carbon sources

Alignments for a candidate for actP in Chlorobium limicola DSM 245

Align actP-like component of D-alanine uptake system (characterized)
to candidate WP_012466706.1 CLIM_RS09040 sodium:solute symporter family protein

Query= reanno::psRCH2:GFF346
         (589 letters)



>NCBI__GCF_000020465.1:WP_012466706.1
          Length = 594

 Score =  699 bits (1803), Expect = 0.0
 Identities = 362/607 (59%), Positives = 441/607 (72%), Gaps = 36/607 (5%)

Query: 3   QYWINMLFVGASFLLYIGIAVWARAGSTKEFYVAGGGVHPVTNGMATAADWMSAASFISM 62
           Q W   + VGA+FL+YI IA+WA+AGSTKEFYVAG GV P+ NGMATAADWMSAASFISM
Sbjct: 4   QTW-TYIIVGATFLIYIAIAIWAKAGSTKEFYVAGAGVPPIINGMATAADWMSAASFISM 62

Query: 63  AGLIASGGYATSVYLMGWTGGYVLLAMLLAPYLRKFGKFTVPDFIGDRFYSRGARLTAVV 122
           AGLI+  GY  SVYLMGWTGGYVLLA+LLAPYLRKFGKFTVPDF+GDR+YS  AR  AV+
Sbjct: 63  AGLISFMGYDGSVYLMGWTGGYVLLALLLAPYLRKFGKFTVPDFVGDRYYSNVARTVAVI 122

Query: 123 CLILISVTYVIGQMAGAGVAFSRFLEVSNSAGIWIAAAIVFAYAVFGGMKGITYTQVAQY 182
           C I +S TYV GQM G GV FSRFLEV  + GI +   IVF YAV GGMKGITYTQVAQY
Sbjct: 123 CAIFVSFTYVAGQMRGVGVVFSRFLEVDINTGILLGMGIVFFYAVLGGMKGITYTQVAQY 182

Query: 183 IVLIIAYTIPAVFIAMQLTGNPIPMFGMFGTHVDSGVPLLDKLDQVVTDLGFAAYTADVD 242
            VLI AY +PA+F+++ + GNPIP FGM G   D GV LLDKLD +   LGFAAYT    
Sbjct: 183 WVLIFAYMVPAIFLSIMIAGNPIPQFGMGGAGSD-GVYLLDKLDGLHQQLGFAAYTTGSK 241

Query: 243 NKLNMFLFTLSLMIGTAGLPHVIIRFFTVPKVADARWSAGWTLVFIALLYLTAPAVASMA 302
             +++F  T++LM+GTAGLPHVI+RFFTVP+V DAR SAGW L+FIALLY TAPA+A+ A
Sbjct: 242 PMIDVFAITVALMVGTAGLPHVIVRFFTVPRVRDARISAGWALIFIALLYTTAPAIATFA 301

Query: 303 RLNLVNTIYPEGPQAEAIRYEDRPEWVQTWERTGLIKWEDKNADGRVQMYNDANA----- 357
           RLNL+ T+           Y D P W + WE+TGL+ W DKN DG++Q Y   NA     
Sbjct: 302 RLNLIQTVSNNS-------YTDMPGWFKKWEKTGLLAWMDKNNDGKIQ-YTGKNAGGGDP 353

Query: 358 ------KFTPTATERGW---------NGNELTVNNDIIVLANPEIANLPGWVIGLIAAGA 402
                 +FT    + G          N NEL ++ DI+VLANPEI NLP WVI L+AAG 
Sbjct: 354 FEGKKPEFTKEKGQHGELLMSNKPTDNSNELFIDKDIMVLANPEIGNLPNWVIALVAAGG 413

Query: 403 IAAALSTAAGLLLAISSAISHDLIKTLINPKISEKNEMLAARLSMTAAILLATWLGLNPP 462
           +AAALSTAAGLLL IS++ISHDLIK  INP ISEK E++ AR+++  AI++A + G+NPP
Sbjct: 414 LAAALSTAAGLLLVISTSISHDLIKKQINPNISEKGELMYARIAVGVAIVVAGYFGINPP 473

Query: 463 GFAAQVVALAFGLAAASLFPALMMGIFSKRVNSKGAVAGMLVGVISTAVYIFLYLGWFFI 522
           GF A+VVA AFGLAAAS FP +++GIFSKR+N +GA++GM+ G++ TA YI  +   F  
Sbjct: 474 GFVAEVVAFAFGLAAASFFPVIILGIFSKRMNKEGAISGMITGLLFTAAYIVYFK--FIS 531

Query: 523 PGTASIPNTPDQWWMGISPQAFGAVGAMLNFAVAYAVSMATEAPPQEIQDLVESVRTPKG 582
           P      N P+ WW GISP+  G +G ++N AV++ VS  T APPQEIQ+LV+S+R PKG
Sbjct: 532 PDM----NKPEFWWFGISPEGIGTLGMLINVAVSFVVSRITPAPPQEIQELVDSLRYPKG 587

Query: 583 AGVALDH 589
           AG A  H
Sbjct: 588 AGEASAH 594


Lambda     K      H
   0.324    0.137    0.419 

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: 1122
Number of extensions: 56
Number of successful extensions: 6
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: 589
Length of database: 594
Length adjustment: 37
Effective length of query: 552
Effective length of database: 557
Effective search space:   307464
Effective search space used:   307464
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 (21.6 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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