GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rhaT' in Alkalihalobacterium alkalinitrilicum DSM 22532

Align RhaT, component of Rhamnose porter (Richardson et al., 2004) (Transport activity is dependent on rhamnokinase (RhaK; AAQ92412) activity (Richardson and Oresnik, 2007) This could be an example of group translocation!) (characterized)
to candidate WP_078427103.1 BK574_RS00955 ABC transporter ATP-binding protein

Query= TCDB::Q7BSH4
         (512 letters)



>NCBI__GCF_002019605.1:WP_078427103.1
          Length = 509

 Score =  288 bits (738), Expect = 2e-82
 Identities = 166/486 (34%), Positives = 275/486 (56%), Gaps = 15/486 (3%)

Query: 20  ILEMRGISQIFPGVKALDNVSIALHPGTVTALIGENGAGKSTLVKILTGIYRPNEGEILV 79
           ++EM+ I + FPG+ A DNV++ +  G + AL+GENGAGKSTL+ +L G+Y+P +GEILV
Sbjct: 4   VIEMKDIRKEFPGIVANDNVTLQVKQGEIHALLGENGAGKSTLMNVLFGLYQPEKGEILV 63

Query: 80  DGRPTTFASAQAAIDAGVTAIHQETVLFDELTVAENIFLGHAPRTRFRTIDWQTMNSRSK 139
            G+P        A   G+  +HQ  +L ++ TV ENI LG  P    +      +   +K
Sbjct: 64  KGKPVKITDPNVANRLGIGMVHQHFMLVEKFTVTENIILGKEPTAGGKI----NIKKAAK 119

Query: 140 ALLTALES---NIDPTIRLKDLSIAQRHLVAIARALSIEARIVIMDEPTAALSRKEIDDL 196
           A+ T  +     +DP  +++D+S+  +  V I + L   A I+I DEPTAAL+ +EI +L
Sbjct: 120 AVETISKQYGLAVDPYAKIQDISVGMQQRVEILKTLYRGAEILIFDEPTAALTPQEITEL 179

Query: 197 FRIVRGLKEQGKAILFISHKFDELYEIADDFVVFPRRSRRPVRGVSRKTPQDEIVRMMVG 256
            +I++ L  +GK+I+ I+HK  E+ E+ D   V  R        +S  TP D +  MMVG
Sbjct: 180 IQIMKKLVSEGKSIILITHKLKEIMEVCDRCTVIRRGRGIGTVDISESTP-DSLAAMMVG 238

Query: 257 RDVENVFPKIDVAIGGPVLEIRNYSHR-----TEFRDISFTLRKGEILGVYGLIGAGRSE 311
           R+V     K        VL+I++   +     T   D+   +  GEILGV G+ G G++E
Sbjct: 239 REVNFSVEKDPAQPKDAVLQIKDLVVKDSRDITAVNDLHLEVHAGEILGVAGVDGNGQTE 298

Query: 312 LSQSLFGITKPLSGKMVLEGQEITIHSPQDAIRAGIVYVPEERGRHGLALPMPIFQNMTL 371
           L +++ G+ KP  G + L GQ+IT  +P+    AG+ ++P++R +HGL L   + +N+ L
Sbjct: 299 LIEAITGLRKPTGGNIQLNGQDITGLTPRKITGAGVGHIPQDRHKHGLVLDFTVGENIVL 358

Query: 372 PSLART--SRRGFLRAANEFALARKYAERLDLRAAALSVPVGTLSGGNQQKVVIGKWLAT 429
            +  +   S  G L     +  A +  E  D+R  +       LSGGNQQK +I + +  
Sbjct: 359 QTYYQKPYSTSGVLNFNEIYKKANELIEDYDVRTPSEHTLARALSGGNQQKAIIAREVDR 418

Query: 430 APKVIILDEPTKGIDIGSKAAVHGFISELAAEGLSIIMVSSELPEIIGMSDRVLVMKEGL 489
           +P ++I  +PT+G+D+G+  ++H  + +   +G +++++S EL E++ +SDR+ V+ EG 
Sbjct: 419 SPDLLIAAQPTRGLDVGAIESIHHRLVKERDKGKAVLLISLELDEVLNVSDRIAVIYEGK 478

Query: 490 SAGIFE 495
              I +
Sbjct: 479 IVAIVD 484



 Score = 84.0 bits (206), Expect = 1e-20
 Identities = 60/225 (26%), Positives = 113/225 (50%), Gaps = 10/225 (4%)

Query: 288 DISFTLRKGEILGVYGLIGAGRSELSQSLFGITKPLSGKMVLEGQEITIHSPQDAIRAGI 347
           +++  +++GEI  + G  GAG+S L   LFG+ +P  G+++++G+ + I  P  A R GI
Sbjct: 22  NVTLQVKQGEIHALLGENGAGKSTLMNVLFGLYQPEKGEILVKGKPVKITDPNVANRLGI 81

Query: 348 VYVPEERGRHGLALPMPIFQNMTLPSLARTSRRGFLRAANEFA--LARKYAERLDLRAAA 405
             V +      L     + +N+ L        +  ++ A +    ++++Y   +D  A  
Sbjct: 82  GMVHQH---FMLVEKFTVTENIILGKEPTAGGKINIKKAAKAVETISKQYGLAVDPYAKI 138

Query: 406 LSVPVGTLSGGNQQKVVIGKWLATAPKVIILDEPTKGIDIGSKAAVHGFISELAAEGLSI 465
             + VG      QQ+V I K L    +++I DEPT  +       +   + +L +EG SI
Sbjct: 139 QDISVGM-----QQRVEILKTLYRGAEILIFDEPTAALTPQEITELIQIMKKLVSEGKSI 193

Query: 466 IMVSSELPEIIGMSDRVLVMKEGLSAGIFERAELSPEALVRAATG 510
           I+++ +L EI+ + DR  V++ G   G  + +E +P++L     G
Sbjct: 194 ILITHKLKEIMEVCDRCTVIRRGRGIGTVDISESTPDSLAAMMVG 238


Lambda     K      H
   0.320    0.137    0.382 

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: 609
Number of extensions: 31
Number of successful extensions: 9
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: 512
Length of database: 509
Length adjustment: 35
Effective length of query: 477
Effective length of database: 474
Effective search space:   226098
Effective search space used:   226098
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 Apr 09 2024. 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