Alignments for a candidate for actP in Oleispira antarctica

GapMind for catabolism of small carbon sources

Alignments for a candidate for actP in Oleispira antarctica

Align Sodium: solute symporter family protein (characterized, see rationale)
to candidate WP_046010589.1 OLEAN_RS19290 cation acetate symporter

Query= uniprot:E4PHQ0
         (588 letters)



>NCBI__GCF_000967895.1:WP_046010589.1
          Length = 576

 Score =  756 bits (1953), Expect = 0.0
 Identities = 385/585 (65%), Positives = 463/585 (79%), Gaps = 16/585 (2%)

Query: 6   INIIFVGGSFLLYIAIAIWAKAGSTSDFYVAGGGVHPITNGAAIGADWMSAASFISMAGL 65
           +  I VG +F +Y+ IA+WA+AGST +FYVAGGG++PI NG A  ADWMSAASFISMAGL
Sbjct: 6   LTYIVVGITFAVYMGIAVWARAGSTKEFYVAGGGINPIANGMATAADWMSAASFISMAGL 65

Query: 66  IAAGGYANSTFLMGWTGGYVLLAMLLAPYLRKFGKFTVPEFIGDRFYSKNARLVAVICLI 125
           IA  GY  S FLMGWTGG+VLLAMLLAPYLRK+GKFTVPEFIGDRFYS+ AR+VAV+CLI
Sbjct: 66  IAFMGYGGSVFLMGWTGGFVLLAMLLAPYLRKYGKFTVPEFIGDRFYSRTARIVAVVCLI 125

Query: 126 VASVTYVIGQMAGAGVAFSRFLEVDSTVGLMIAAVVVFVYAVMGGMKGITYTQVAQYCVL 185
           + SVTYVIGQM G GVAFSRFLEV   +GL+I   +VF YAV+GGMKGITYTQ+AQ+CVL
Sbjct: 126 ICSVTYVIGQMKGIGVAFSRFLEVSYDIGLLIGMFIVFFYAVLGGMKGITYTQIAQFCVL 185

Query: 186 IVAYTIPAVFISLQLTGNPIPGLGLFSTHVDSGMPILSKLNQVITDLGFNEYTADID-NK 244
           I+AYTIPA+FISL LTGNPIP LGL ST + S + +L +L+QV+++LGF EYT     + 
Sbjct: 186 ILAYTIPAIFISLNLTGNPIPQLGLGSTMIGSDVYLLDRLDQVVSELGFAEYTTQARLST 245

Query: 245 LNMVLFTLSLMIGTAGLPHVIIRFFTVPKVADARWSAGWALVFIALLYLTAPAVASMARL 304
           +NM  +T+SLMIGTAGLPHVIIRFFTVPKV DAR SA WAL+FI++LY TAPAVA MARL
Sbjct: 246 VNMFAYTMSLMIGTAGLPHVIIRFFTVPKVKDARASAFWALIFISILYTTAPAVAGMARL 305

Query: 305 NLMTTIYPDGTSAEPIQYDERPNWIKEWEITGLIQFTDKNEDGRIQLYNDSEAFAPTAEA 364
           N++ TI  + T +E ++YDERP W K WE TGL++F DKN DGRIQ   D E        
Sbjct: 306 NMINTI--ETTQSENLKYDERPQWFKNWEKTGLLKFEDKNGDGRIQYVADPEK------- 356

Query: 365 RGWNGNELV-VNRDILVLANPEIANLPGWVIGLIAAGGLAAALSTAAGLLLAISSAVSHD 423
                NE+V ++RDI+VLANPEIA LP WVI L+AAGGLAAALSTAAGLLLAI+SA+SHD
Sbjct: 357 -----NEMVKIDRDIMVLANPEIAQLPNWVIALVAAGGLAAALSTAAGLLLAIASAISHD 411

Query: 424 LIKGSINPAISEKGELLAARISMAVAIVVATYLGANPPGFAAQVVALAFGIAAASLFPAL 483
           L+KG   P I+EK ELLA+R++MA AIV A YLG NPP FAA  VALAFG+AA+S+FPAL
Sbjct: 412 LLKGVFAPNITEKQELLASRVAMAAAIVGAGYLGFNPPDFAAGTVALAFGLAASSIFPAL 471

Query: 484 MMGIFSKRVNNTGAIAGMLSGLTFTLVYIFVYKGWLFIPGTNNLPDTPDNWVLGISPLSI 543
           MMGIFSKR+N  GAIAGM+SG+T TL+Y+F +KG +F+  T+ L D P NW  GI P + 
Sbjct: 472 MMGIFSKRINKEGAIAGMISGITVTLLYVFQHKGIMFVADTSFLGDMPANWFFGIEPNAF 531

Query: 544 GAIGAIVNFAVAFIVSNATEEPPVEIQELVESVRYPRGAGQAQDH 588
           G IGA+VNF+VA +VS  T EPP E+Q+LVE +R P G  +A DH
Sbjct: 532 GVIGAVVNFSVANLVSRVTAEPPQEVQDLVEHIRVPCGVEEAHDH 576


Lambda     K      H
   0.323    0.138    0.413 

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: 1082
Number of extensions: 43
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: 588
Length of database: 576
Length adjustment: 36
Effective length of query: 552
Effective length of database: 540
Effective search space:   298080
Effective search space used:   298080
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 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 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