GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_11890 in Pseudovibrio axinellae Ad2

Align m-Inositol ABC transporter, ATPase component (itaA) (characterized)
to candidate WP_068000812.1 PsAD2_RS00245 ABC transporter ATP-binding protein

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



>NCBI__GCF_001623255.1:WP_068000812.1
          Length = 514

 Score =  299 bits (765), Expect = 2e-85
 Identities = 180/506 (35%), Positives = 288/506 (56%), Gaps = 22/506 (4%)

Query: 28  LEIINVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAGELRLR 87
           +E+I V+K F  V A  D+ L V  GS+  ++GENGAGKSTLM I+ G Y  D+G +++ 
Sbjct: 9   IELIGVNKSFGPVHANKDIDLVVGKGSIHGIIGENGAGKSTLMSILYGFYHADSGTIKID 68

Query: 88  GKPVTFDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNGFHMID-----HREMH 142
           GK  T     +A+  GI M+HQ   L+   ++ EN+ +G E   G  + D      RE+ 
Sbjct: 69  GKATTIPDSKSAISQGIGMVHQHFMLVDPFTVLENVVLGAE--GGALLKDGVANARRELK 126

Query: 143 RCTAQLLERLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITDKEVAH 202
           R    L +   + +DP+  VG L +  +Q VEI KA+   +DILI+DEPT  +T  E  H
Sbjct: 127 R----LADEYDMTIDPDAVVGELPVGLQQRVEILKALYRGADILILDEPTGVLTPSEADH 182

Query: 203 LFSIIADLKAQGKGIIYITHKMNEVFSIADEVAVFRDGAYIGLQRADSMDGDSLISMMVG 262
           LF I+  L+ QGK ++ ITHK+ E+  + D V+V R G  +  ++      + L  +MVG
Sbjct: 183 LFRILRVLRDQGKTVLLITHKLREIMDVTDTVSVMRRGEMVASRKTAQTSMEELAELMVG 242

Query: 263 RELSQLFPVREKPIGDLLMSVRDLRLD---GV--FKGVSFDLHAGEILGIAGLMGSGRTN 317
           R +       +  +G  L+ V  L +    GV   K VSF++ AGE+LGIAG+ G+G++ 
Sbjct: 243 RSVLLEVSKPDVEVGKPLLKVEGLNVKDERGVRRVKDVSFEVRAGEVLGIAGVSGNGQSE 302

Query: 318 VAEAIFGITPSDGGEICLDGQPVRISDPHMAI---EKGFALLTEDRKLSGLFPCLSVLEN 374
           +  A+ GIT ++ G + L GQ + +S+ H A    ++G + + EDR   GL    S  EN
Sbjct: 303 LMAALAGITRAESGSMELAGQKLDLSEVHDAAQMRDRGMSHVPEDRHRMGLVNKFSEAEN 362

Query: 375 MEMAV--LPHYAGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARW 432
             +       Y+   F+ + A+R   ++  +K  ++ P  E      SGGNQQK +LAR 
Sbjct: 363 SILGYHRESKYSKGMFLDKDAIRKEAKERIEKYDIRPPLTEMTAAKFSGGNQQKIVLARE 422

Query: 433 LMTNPRILILDEPTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMH 492
           +  NP +L++ +PTRG+D+GA   I+  I  + ++G AV+++S EL E+  +SDR++VM 
Sbjct: 423 IECNPDVLLIGQPTRGVDIGAIEYIHNRIMDMRAQGKAVLLVSVELDEIRSLSDRIIVMF 482

Query: 493 EGDLMGTLDRSEATQERVMQLASGMS 518
           +G+++G     EAT++ +  L +G++
Sbjct: 483 DGNVVGERG-PEATEQDLGLLMAGVN 507



 Score = 85.1 bits (209), Expect = 6e-21
 Identities = 61/230 (26%), Positives = 111/230 (48%), Gaps = 12/230 (5%)

Query: 293 KGVSFDLHAGEILGIAGLMGSGRTNVAEAIFGITPSDGGEICLDGQPVRISDPHMAIEKG 352
           K +   +  G I GI G  G+G++ +   ++G   +D G I +DG+   I D   AI +G
Sbjct: 25  KDIDLVVGKGSIHGIIGENGAGKSTLMSILYGFYHADSGTIKIDGKATTIPDSKSAISQG 84

Query: 353 FALLTEDRKLSGLFPCLSVLENMEMAVLPHYAGNGFIQQKALRALCEDMCKKLRVK---T 409
             ++ +   L   F   +VLEN+ +       G   ++     A  E   K+L  +   T
Sbjct: 85  IGMVHQHFMLVDPF---TVLENVVLGA----EGGALLKDGVANARRE--LKRLADEYDMT 135

Query: 410 PSLEQCIDTLSGGNQQKALLARWLMTNPRILILDEPTRGIDVGAKAEIYRLISYLASEGM 469
              +  +  L  G QQ+  + + L     ILILDEPT  +       ++R++  L  +G 
Sbjct: 136 IDPDAVVGELPVGLQQRVEILKALYRGADILILDEPTGVLTPSEADHLFRILRVLRDQGK 195

Query: 470 AVIMISSELPEVLGMSDRVMVMHEGDLMGTLDRSEATQERVMQLASGMSV 519
            V++I+ +L E++ ++D V VM  G+++ +   ++ + E + +L  G SV
Sbjct: 196 TVLLITHKLREIMDVTDTVSVMRRGEMVASRKTAQTSMEELAELMVGRSV 245


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: 637
Number of extensions: 31
Number of successful extensions: 8
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: 521
Length of database: 514
Length adjustment: 35
Effective length of query: 486
Effective length of database: 479
Effective search space:   232794
Effective search space used:   232794
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.

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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:

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