Alignments for a candidate for rhaT' in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Alignments for a candidate for rhaT' in Dinoroseobacter shibae DFL-12

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 3609459 Dshi_2843 ABC transporter related (RefSeq)

Query= TCDB::Q7BSH4
         (512 letters)



>FitnessBrowser__Dino:3609459
          Length = 548

 Score =  271 bits (692), Expect = 6e-77
 Identities = 185/505 (36%), Positives = 276/505 (54%), Gaps = 27/505 (5%)

Query: 17  APAILEMRGISQIFPGVKALDNVSIALHPGTVTALIGENGAGKSTLVKILTGIYRPNEGE 76
           APAI E+RGIS+ F  V+A  ++SI + PGT+  +IGENGAGKSTL+ IL G Y+ + GE
Sbjct: 23  APAI-ELRGISKAFGPVQANKDISIRVMPGTIHGIIGENGAGKSTLMSILYGFYKADAGE 81

Query: 77  ILVDGRPTTFASAQAAIDAGVTAIHQETVLFDELTVAENIFLGHAPRTRFRTIDWQTMNS 136
           I + G+ T    +QAAI AG+  + Q   L +  TV EN+ LG       R        +
Sbjct: 82  IFIKGQKTEIPDSQAAIRAGIGMVFQHFKLVENFTVLENVVLGAEEGALLR-----PSLA 136

Query: 137 RSKALLTAL----ESNIDPTIRLKDLSIAQRHLVAIARALSIEARIVIMDEPTAALSRKE 192
           +++ LL  L    E N+ P   ++DLS+  +  V I +AL  +A I+I+DEPT  L+  E
Sbjct: 137 KARKLLRELSEEYELNVAPDALIEDLSVGHQQRVEILKALYRKADILILDEPTGVLTPAE 196

Query: 193 IDDLFRIVRGLKEQGKAILFISHKFDELYEIADDFVVFPRRSRRPVRGVSRKTPQDEIVR 252
            D LFRI+ GLK +GK I+ I+HK  E+ E  D   V  RR        +  T  +++  
Sbjct: 197 ADHLFRILEGLKAEGKTIILITHKLREIMETTDTVSVM-RRGEMTATVKTADTSPEQLAE 255

Query: 253 MMVGRDVENVFPKIDVAIGGPVLEIRNY-----SHRTEFRDISFTLRKGEILGVYGLIGA 307
           +MVGR V     K     G P+L + +            + IS  +R GE+LG+ G+ G 
Sbjct: 256 LMVGRKVLLRVDKTPAQPGAPILTVDDLRVVDDQGVERVKGISLQVRAGEVLGIAGVAGN 315

Query: 308 GRSELSQSLFGITKPLSGKMVLEGQEITI---HSPQDAIRA-GIVYVPEERGRHGLALPM 363
           G+SEL + L G+ +P +G++ + GQ+I +   HS     RA GI +VPE+R   GL +  
Sbjct: 316 GQSELLEVLGGM-RPATGRVTVSGQQIDLTGKHSNGKTRRAQGIAHVPEDRQAEGLIMDY 374

Query: 364 PIFQNMTLPSLARTS-RRGFL---RAANEFALARKYAERLDLRAAALSVPVGTLSGGNQQ 419
             ++N+        +  RG L   RA    A A     R D+R A   +     SGGNQQ
Sbjct: 375 HAWENVAFGYHDDPAYNRGLLMDNRAVR--ADAEGKIARFDVRPADCWLAAKNFSGGNQQ 432

Query: 420 KVVIGKWLATAPKVIILDEPTKGIDIGSKAAVHGFISELAAEGLSIIMVSSELPEIIGMS 479
           K+V+ + +   P+++++ +PT+G+DIG+   +H  I  L   G +I++VS EL EI+ +S
Sbjct: 433 KIVLAREIERNPELLLVGQPTRGVDIGAIEFIHQQIIALRDAGKAILLVSVELEEILSLS 492

Query: 480 DRVLVMKEGLSAGIFERAELSPEAL 504
           DRV VM +G   G    AE + + L
Sbjct: 493 DRVAVMFDGRIMGERPAAETNEKEL 517



 Score = 95.9 bits (237), Expect = 3e-24
 Identities = 77/242 (31%), Positives = 119/242 (49%), Gaps = 10/242 (4%)

Query: 273 PVLEIRNYSHR----TEFRDISFTLRKGEILGVYGLIGAGRSELSQSLFGITKPLSGKMV 328
           P +E+R  S         +DIS  +  G I G+ G  GAG+S L   L+G  K  +G++ 
Sbjct: 24  PAIELRGISKAFGPVQANKDISIRVMPGTIHGIIGENGAGKSTLMSILYGFYKADAGEIF 83

Query: 329 LEGQEITIHSPQDAIRAGIVYVPEERGRHGLALPMPIFQNMTLPSLARTSRRGFLRAANE 388
           ++GQ+  I   Q AIRAGI  V +      L     + +N+ L +      R  L  A +
Sbjct: 84  IKGQKTEIPDSQAAIRAGIGMVFQH---FKLVENFTVLENVVLGAEEGALLRPSLAKARK 140

Query: 389 FALARKYAERLDLRAAALSVPVGTLSGGNQQKVVIGKWLATAPKVIILDEPTKGIDIGSK 448
             L R+ +E  +L  A  ++ +  LS G+QQ+V I K L     ++ILDEPT  +     
Sbjct: 141 --LLRELSEEYELNVAPDAL-IEDLSVGHQQRVEILKALYRKADILILDEPTGVLTPAEA 197

Query: 449 AAVHGFISELAAEGLSIIMVSSELPEIIGMSDRVLVMKEGLSAGIFERAELSPEALVRAA 508
             +   +  L AEG +II+++ +L EI+  +D V VM+ G      + A+ SPE L    
Sbjct: 198 DHLFRILEGLKAEGKTIILITHKLREIMETTDTVSVMRRGEMTATVKTADTSPEQLAELM 257

Query: 509 TG 510
            G
Sbjct: 258 VG 259


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: 674
Number of extensions: 44
Number of successful extensions: 11
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 512
Length of database: 548
Length adjustment: 35
Effective length of query: 477
Effective length of database: 513
Effective search space:   244701
Effective search space used:   244701
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 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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:

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