GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_11890 in Rhodobacter johrii JA192

Align m-Inositol ABC transporter, ATPase component (itaA) (characterized)
to candidate WP_069332735.1 C8J29_RS16570 sugar ABC transporter ATP-binding protein

Query= reanno::pseudo3_N2E3:AO353_21385
         (521 letters)



>NCBI__GCF_003046325.1:WP_069332735.1
          Length = 499

 Score =  379 bits (972), Expect = e-109
 Identities = 214/494 (43%), Positives = 299/494 (60%), Gaps = 3/494 (0%)

Query: 27  LLEIINVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAGELRL 86
           +L I  VS+ F  V  L DV   +RPG V AL+GENGAGKST MKI+AG   P AGE+ L
Sbjct: 5   VLAIRQVSRLFGPVQVLFDVDFDLRPGEVHALIGENGAGKSTTMKILAGYLAPSAGEVLL 64

Query: 87  RGKPVTFDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNGFHMIDHREMHRCTA 146
            G+PV F +   A  AG+ MIHQE NL   +++ ENI++GRE   G   +DHR M   + 
Sbjct: 65  DGRPVHFPSSREAEAAGVVMIHQEFNLATPLTVEENIFLGRELKRG-PFLDHRAMQAESR 123

Query: 147 QLLERLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITDKEVAHLFSI 206
           +LLERL   +DP  +V  LS+  RQMVEIAKA+   + +LIMDEPT+ +T +E   L   
Sbjct: 124 RLLERLHCAVDPRARVSTLSVPNRQMVEIAKALGLKARVLIMDEPTAVLTHRETDTLLEQ 183

Query: 207 IADLKAQGKGIIYITHKMNEVFSIADEVAVFRDGAYIGLQRADSMDGDSLISMMVGRELS 266
           +  L+A G  I+Y +HK++EV  IAD V V RDG  +    A  +  D +   MVGRELS
Sbjct: 184 VDRLRAAGTAILYTSHKLDEVARIADRVTVLRDGRRVMTAPAKGLSEDRMAETMVGRELS 243

Query: 267 QLFPVREKPIGDLLMSVRDLRLDGVFKGVSFDLHAGEILGIAGLMGSGRTNVAEAIFGIT 326
            LFP +  P  + ++ V  L + G  +  SF L  GE+LG AGL+GSGRT + E I G+ 
Sbjct: 244 GLFPPKSSPAPEPVLEVAGLTVPGFVRDASFTLRRGEVLGFAGLVGSGRTELMEGIVGLR 303

Query: 327 PSDGGEICLDGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHYAGN 386
           P+  GE+ ++G P+  +    A   G   LTEDRK  GL     + EN+ +  L  + G 
Sbjct: 304 PAT-GEVRMEGSPLPHASVSAARAAGLVYLTEDRKEKGLLLGKPLGENLTLLALDRF-GR 361

Query: 387 GFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRILILDEPT 446
             I + A             ++         +LSGGNQQK LLA+ ++  PR++I+DEPT
Sbjct: 362 VLIDKAAEERALTQAISDFDIRVGDRGISAGSLSGGNQQKLLLAKTMLAEPRVVIIDEPT 421

Query: 447 RGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEGDLMGTLDRSEAT 506
           RGIDVG K +IY  I+ LA+EG +VI++SSELPEV+G+++RV+VM  G + G ++    T
Sbjct: 422 RGIDVGTKQQIYGFIARLAAEGRSVIVVSSELPEVIGLANRVVVMSAGRIAGEVEGEAIT 481

Query: 507 QERVMQLASGMSVR 520
           +E +++LA G++ R
Sbjct: 482 EENIVRLAMGLNHR 495


Lambda     K      H
   0.321    0.137    0.391 

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: 642
Number of extensions: 31
Number of successful extensions: 10
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: 521
Length of database: 499
Length adjustment: 34
Effective length of query: 487
Effective length of database: 465
Effective search space:   226455
Effective search space used:   226455
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.6 bits)

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

Links

Downloads

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:

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:

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:

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:

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