Alignments for a candidate for rbsA in Trichormus variabilis ATCC 29413

GapMind for catabolism of small carbon sources

Alignments for a candidate for rbsA in Trichormus variabilis ATCC 29413

Align ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 (characterized)
to candidate WP_011318959.1 AVA_RS10980 sugar ABC transporter ATP-binding protein

Query= CharProtDB::CH_003578
         (501 letters)



>NCBI__GCF_000204075.1:WP_011318959.1
          Length = 517

 Score =  428 bits (1100), Expect = e-124
 Identities = 229/495 (46%), Positives = 330/495 (66%), Gaps = 7/495 (1%)

Query: 4   LLQLKGIDKAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGTLLW 63
           +L+++GI K F GV AL G  L +YPG V AL+GENGAGKST+MK+L G Y  D G +  
Sbjct: 18  VLEMQGIAKRFHGVPALQGVNLTIYPGEVHALMGENGAGKSTLMKILAGAYIADEGEIRI 77

Query: 64  LGKETTFTGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREFVNRFGKIDWKTMYAEAD 123
            GK    T P ++++AGI +I+QELN+ P LT+ ENIF+G E + R   +D K M  EA 
Sbjct: 78  NGKGVKITDPGTARQAGINLIYQELNVAPNLTVTENIFMGSE-LTRGQFLDRKAMELEAQ 136

Query: 124 KLLAKLNLRFKSDKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESLFRV 183
           ++LA L   F    +VG L+I +QQ VEIA+ L   S++++MDEPT AL+D ETE LF V
Sbjct: 137 QVLASLGASFAPTDIVGTLAIAEQQQVEIARALKDNSRILVMDEPTAALSDRETERLFEV 196

Query: 184 IRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTEDSLIEMMVGRKLE 243
           IR+L++ G  I+YISHRM+EI+ + D ++V RDGQ+I       ++   L++MMVGR ++
Sbjct: 197 IRKLRNDGIAIIYISHRMEEIYALADRISVLRDGQYIGSLTREEISPQRLVQMMVGRSMQ 256

Query: 244 DQYPHLDKA-PGDIRLKVDNLC-GPGVNDVSFTLRKGEILGVSGLMGAGRTELMKVLYGA 301
           D Y H  ++ PG + L+V N+  G  V   SF LR GEILG++GL+GAGRTE+ ++++GA
Sbjct: 257 DFYEHQRQSNPGPVVLEVRNISDGRKVQPASFQLRAGEILGLAGLVGAGRTEVSRLIFGA 316

Query: 302 LPRTSGYVTLDGHEVVTRSPQDGLANGIVYISEDRKRDGLVLGMSVKENMSLTALRYFSR 361
             + SG V L+G ++   SP D +A GI Y+ EDRK  GL L MS ++N+ L  L+  + 
Sbjct: 317 DRKVSGEVFLNGKKLEIHSPSDAIAVGIGYVPEDRKDQGLFLEMSSRKNIGLNRLKQDAN 376

Query: 362 AGGSLKHADEQQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAIARGLMTRPKVLILDE 421
             G +      +  +D +  F+++  ++E     LSGGNQQK+ +AR L   P+VL+LDE
Sbjct: 377 L-GIVNWGSVNKIATDAVENFHIRLANLEIRAVDLSGGNQQKLLLARWLAINPRVLMLDE 435

Query: 422 PTRGVDVGAKKEIYQLINQFKADGLSIILVSSEMPEVLGMSDRIIVMHEGHLSGEFTR-- 479
           PTRGVD+GAK EIY++I+   A G++I++VSSE+PE++G+SDR++VM EG L GE     
Sbjct: 436 PTRGVDIGAKSEIYRIISDLSAQGVAILMVSSELPEIVGLSDRVLVMREGQLVGELDNSI 495

Query: 480 -EQATQEVLMAAAVG 493
            ++ TQE +M  A G
Sbjct: 496 GKEITQENIMHYATG 510



 Score =  101 bits (251), Expect = 7e-26
 Identities = 66/233 (28%), Positives = 117/233 (50%), Gaps = 15/233 (6%)

Query: 266 PGVNDVSFTLRKGEILGVSGLMGAGRTELMKVLYGALPRTSGYVTLDGHEVVTRSPQDGL 325
           P +  V+ T+  GE+  + G  GAG++ LMK+L GA     G + ++G  V    P    
Sbjct: 32  PALQGVNLTIYPGEVHALMGENGAGKSTLMKILAGAYIADEGEIRINGKGVKITDPGTAR 91

Query: 326 ANGIVYISEDRKRDGLVLGMSVKENM----SLTALRYFSRAGGSLKHADEQQAVSDFIRL 381
             GI  I ++     +   ++V EN+     LT  ++  R    L   + QQ ++     
Sbjct: 92  QAGINLIYQELN---VAPNLTVTENIFMGSELTRGQFLDRKAMEL---EAQQVLASLGAS 145

Query: 382 FNVKTPSMEQAIGLLSGGNQQKVAIARGLMTRPKVLILDEPTRGVDVGAKKEIYQLINQF 441
           F     +    +G L+   QQ+V IAR L    ++L++DEPT  +     + ++++I + 
Sbjct: 146 F-----APTDIVGTLAIAEQQQVEIARALKDNSRILVMDEPTAALSDRETERLFEVIRKL 200

Query: 442 KADGLSIILVSSEMPEVLGMSDRIIVMHEGHLSGEFTREQATQEVLMAAAVGK 494
           + DG++II +S  M E+  ++DRI V+ +G   G  TRE+ + + L+   VG+
Sbjct: 201 RNDGIAIIYISHRMEEIYALADRISVLRDGQYIGSLTREEISPQRLVQMMVGR 253


Lambda     K      H
   0.318    0.137    0.380 

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: 41
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: 501
Length of database: 517
Length adjustment: 34
Effective length of query: 467
Effective length of database: 483
Effective search space:   225561
Effective search space used:   225561
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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:

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 2024 update 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