Alignments for a candidate for actP in Rhodobacter ovatus JA234

GapMind for catabolism of small carbon sources

Alignments for a candidate for actP in Rhodobacter ovatus JA234

Align actP-like component of D-alanine uptake system (characterized)
to candidate WP_097029692.1 CRO07_RS05565 cation acetate symporter

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



>NCBI__GCF_900207575.1:WP_097029692.1
          Length = 654

 Score =  796 bits (2055), Expect = 0.0
 Identities = 418/654 (63%), Positives = 488/654 (74%), Gaps = 65/654 (9%)

Query: 1   MSQYWINMLFVGASFLLYIGIAVWARAGSTKEFYVAGGGVHPVTNGMATAADWMSAASFI 60
           M Q+ +N++ VG +F +Y+GIA+WARAGST EFY AG GVHPV NGMAT ADWMSAASFI
Sbjct: 1   MDQFTLNLIVVGITFAIYVGIAIWARAGSTAEFYAAGQGVHPVLNGMATGADWMSAASFI 60

Query: 61  SMAGLIA---SGGYATSVYLMGWTGGYVLLAMLLAPYLRKFGKFTVPDFIGDRFYSRGAR 117
           SMAG+IA   +GGY  S +LMGWTGGYVLLA+LLAPYLRKFGKFTVP+FIGDRFYS GAR
Sbjct: 61  SMAGIIALAPAGGYTQSAFLMGWTGGYVLLALLLAPYLRKFGKFTVPEFIGDRFYSGGAR 120

Query: 118 LTAVVCLILISVTYVIGQMAGAGVAFSRFLEVSNSAGIWIAAAIVFAYAVFGGMKGITYT 177
           L  V+CLI+IS+TYVIGQM G GV FSRFLEVS   G++I AAIVFAYAVFGGMKGITYT
Sbjct: 121 LLGVICLIVISLTYVIGQMRGVGVTFSRFLEVSTDMGLYIGAAIVFAYAVFGGMKGITYT 180

Query: 178 QVAQYIVLIIAYTIPAVFIAMQLTGNPIPMFGMFGTHVDSG--VPLLDKLDQVVTDLGFA 235
           QVAQY+VLIIAYTIPA+FI++ LTG+ +P  G+ G +  +      L KLD VVT+LGF 
Sbjct: 181 QVAQYVVLIIAYTIPAIFISLALTGSFLPQMGLIGDYAPAAGDQAFLAKLDAVVTELGFT 240

Query: 236 AYTADVDNKLNMFLFTLSLMIGTAGLPHVIIRFFTVPKVADARWSAGWTLVFIALLYLTA 295
           AYTAD  N LNMFLFT+SLMIGTAGLPHVIIRFFTVPKVADAR SAGW+LVFIALLY  A
Sbjct: 241 AYTADTTNMLNMFLFTMSLMIGTAGLPHVIIRFFTVPKVADARSSAGWSLVFIALLYTVA 300

Query: 296 PAVASMARLNLVNTIYP----------EGPQAEAIRYEDRPEWVQTWERTGLIKWEDKNA 345
           PAV SMARLN   T++P          E    EAI+ + +  WV+TWE+TGL+  +D N 
Sbjct: 301 PAVGSMARLNFTTTMWPAAVSGNALDGEAVSLEAIQNDPKLNWVKTWEQTGLLVLKDLNG 360

Query: 346 DGRVQMYND----------------------ANAKFT----------------------- 360
           DG +Q +ND                      ANA                          
Sbjct: 361 DGHIQYFNDGKLAAENKAVETATKALTDAKAANADAARIAELEAALLAAEDARKAKGGEV 420

Query: 361 ----PTATERGWNGNELT-VNNDIIVLANPEIANLPGWVIGLIAAGAIAAALSTAAGLLL 415
                T TERGW  +E+  ++NDI+VLANPEIA LPGWVI L+AAGA+AAALSTAAGLLL
Sbjct: 421 TVGGQTLTERGWIASEVVKIDNDIMVLANPEIAALPGWVIALVAAGALAAALSTAAGLLL 480

Query: 416 AISSAISHDLIKTLINPKISEKNEMLAARLSMTAAILLATWLGLNPPGFAAQVVALAFGL 475
           AISSAISHDLIK  INP ISEK E+LAAR+SMT AI++ATWLGLNPPGFAAQVVALAFGL
Sbjct: 481 AISSAISHDLIKGSINPNISEKGELLAARISMTFAIVVATWLGLNPPGFAAQVVALAFGL 540

Query: 476 AAASLFPALMMGIFSKRVNSKGAVAGMLVGVISTAVYIFLYLGWFFIPGTASIPNTPDQW 535
           AAA++FP LMMGIFSKRVN +GA+ GMLVG+I T+VYIFLY GWFFIPGT    + P  +
Sbjct: 541 AAATIFPVLMMGIFSKRVNKEGAIMGMLVGLIFTSVYIFLYKGWFFIPGTEVYADVPANY 600

Query: 536 WMGISPQAFGAVGAMLNFAVAYAVSMATEAPPQEIQDLVESVRTPKGAGVALDH 589
           + GISP + G VGA+LNF VA+AVS  T+APP+E+ DL+ES+R P+GAG A  H
Sbjct: 601 FFGISPLSIGTVGAVLNFVVAFAVSAVTKAPPREVVDLIESIRIPRGAGKATAH 654


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: 1140
Number of extensions: 43
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 589
Length of database: 654
Length adjustment: 37
Effective length of query: 552
Effective length of database: 617
Effective search space:   340584
Effective search space used:   340584
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 Sep 24 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:

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