Alignments for a candidate for rbsA in Acidovorax sp. GW101-3H11

GapMind for catabolism of small carbon sources

Alignments for a candidate for rbsA in Acidovorax sp. GW101-3H11

Align ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 (characterized)
to candidate Ac3H11_2881 Ribose ABC transport system, ATP-binding protein RbsA (TC 3.A.1.2.1)

Query= CharProtDB::CH_003578
         (501 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2881
          Length = 496

 Score =  364 bits (934), Expect = e-105
 Identities = 210/497 (42%), Positives = 301/497 (60%), Gaps = 7/497 (1%)

Query: 1   MEALLQLKGIDKAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGT 60
           M   ++ + + K F  V+ L G    + PGRV  L+GENGAGKST+MK+L G  +   G 
Sbjct: 1   MSVAVEFRNVTKEFGPVRVLHGVGFALQPGRVYGLLGENGAGKSTLMKILAGYESPTTGE 60

Query: 61  LLWLGKETTFTGPKSSQEA-GIGIIHQELNLIPQLTIAENIFLGREFVNRFGKIDWKTMY 119
           ++  G      G   + EA GI +IHQE NL   LTIA+NIFLG E + R   +D K M 
Sbjct: 61  VVVDGAVRAPGGGSRAAEAQGIVLIHQEFNLADDLTIAQNIFLGHE-IKRGLFLDDKAMR 119

Query: 120 AEADKLLAKLNLRFKSDKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETES 179
            +  + LAK+ L    D  V  L + ++Q+VEIA+ L+  ++++IMDEPT  LT  ETE 
Sbjct: 120 EKTREALAKVGLPLDPDTRVRKLIVAEKQLVEIARALARNARLLIMDEPTATLTPGETER 179

Query: 180 LFRVIRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTEDSLIEMMVG 239
           LF ++  LK+ G  I+YISH++ E+    D+V V RDG  +A    AS+T   +  +MVG
Sbjct: 180 LFALMAGLKAAGVTIIYISHKLDEVERTTDEVVVMRDGLLVAREATASVTRRQMANLMVG 239

Query: 240 RKLEDQYPHLDKAPGD--IRLKVDNLCGPG-VNDVSFTLRKGEILGVSGLMGAGRTELMK 296
           R+L D +P    AP D    + V  L  PG    V F +R+GEILG +GL+GAGRTEL +
Sbjct: 240 RELADLFPPKLPAPQDGAPAITVRGLTVPGWAEGVDFEVRRGEILGFAGLVGAGRTELFE 299

Query: 297 VLYGALPRTSGYVTLDGHEVVTRSPQDGLANGIVYISEDRKRDGLVLGMSVKENMSLTAL 356
            L G  PRT+G V + G  V  +SP+D   +G+ Y+SEDRK  GL +   ++ N++L AL
Sbjct: 300 GLLGLRPRTAGTVEIAGQPVQLKSPRDAARHGLTYLSEDRKGKGLHVHFGLRPNLTLMAL 359

Query: 357 RYFSRAGGSLKHADEQQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAIARGLMTRPKV 416
             +++    L  A EQ A+ + ++ F ++T S+E     LSGGNQQK+A+A+ L   P V
Sbjct: 360 ERYAKPW--LDPAAEQAALREAVQEFGIRTGSLEVRASSLSGGNQQKLALAKVLHPGPSV 417

Query: 417 LILDEPTRGVDVGAKKEIYQLINQFKADGLSIILVSSEMPEVLGMSDRIIVMHEGHLSGE 476
           ++LDEPTRGVDVGAK+EIY L+ +    GL++I++SSE+ E++G+  R+ VM  G L   
Sbjct: 418 VVLDEPTRGVDVGAKREIYHLVQRLAEQGLAVIVISSELMELIGLCHRVAVMRAGRLQTT 477

Query: 477 FTREQATQEVLMAAAVG 493
                 T+E L+A A G
Sbjct: 478 LQEPHLTEEELIAHATG 494



 Score = 79.7 bits (195), Expect = 2e-19
 Identities = 68/236 (28%), Positives = 114/236 (48%), Gaps = 24/236 (10%)

Query: 268 VNDVSFTLRKGEILGVSGLMGAGRTELMKVLYGALPRTSGYVTLDGHEVVTRSPQDGL-- 325
           ++ V F L+ G + G+ G  GAG++ LMK+L G    T+G V +DG     R+P  G   
Sbjct: 20  LHGVGFALQPGRVYGLLGENGAGKSTLMKILAGYESPTTGEVVVDG---AVRAPGGGSRA 76

Query: 326 --ANGIVYISEDRKRDGLVLGMSVKENMSLTALRYFSRAGGSLKHAD--EQQAVSDFIR- 380
             A GIV I ++     L   +++ +N+ L         G  +K     + +A+ +  R 
Sbjct: 77  AEAQGIVLIHQEFN---LADDLTIAQNIFL---------GHEIKRGLFLDDKAMREKTRE 124

Query: 381 -LFNVKTP-SMEQAIGLLSGGNQQKVAIARGLMTRPKVLILDEPTRGVDVGAKKEIYQLI 438
            L  V  P   +  +  L    +Q V IAR L    ++LI+DEPT  +  G  + ++ L+
Sbjct: 125 ALAKVGLPLDPDTRVRKLIVAEKQLVEIARALARNARLLIMDEPTATLTPGETERLFALM 184

Query: 439 NQFKADGLSIILVSSEMPEVLGMSDRIIVMHEGHLSGEFTREQATQEVLMAAAVGK 494
              KA G++II +S ++ EV   +D ++VM +G L         T+  +    VG+
Sbjct: 185 AGLKAAGVTIIYISHKLDEVERTTDEVVVMRDGLLVAREATASVTRRQMANLMVGR 240



 Score = 79.0 bits (193), Expect = 4e-19
 Identities = 58/232 (25%), Positives = 102/232 (43%), Gaps = 20/232 (8%)

Query: 22  GAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGTLLWLGKETTFTGPKSSQEAGI 81
           G    V  G ++   G  GAG++ + + L G+  R AGT+   G+      P+ +   G+
Sbjct: 273 GVDFEVRRGEILGFAGLVGAGRTELFEGLLGLRPRTAGTVEIAGQPVQLKSPRDAARHGL 332

Query: 82  GII---------HQELNLIPQLTIAENIFLGREFVNRFGK--IDWKTMYAEADKLLAKLN 130
             +         H    L P LT+          + R+ K  +D     A   + + +  
Sbjct: 333 TYLSEDRKGKGLHVHFGLRPNLTLMA--------LERYAKPWLDPAAEQAALREAVQEFG 384

Query: 131 LRFKSDKL-VGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESLFRVIRELKS 189
           +R  S ++    LS G+QQ + +AKVL     V+++DEPT  +       ++ +++ L  
Sbjct: 385 IRTGSLEVRASSLSGGNQQKLALAKVLHPGPSVVVLDEPTRGVDVGAKREIYHLVQRLAE 444

Query: 190 QGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTEDSLIEMMVGRK 241
           QG  ++ IS  + E+  +C  V V R G+     +   LTE+ LI    G +
Sbjct: 445 QGLAVIVISSELMELIGLCHRVAVMRAGRLQTTLQEPHLTEEELIAHATGTR 496


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: 621
Number of extensions: 33
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 501
Length of database: 496
Length adjustment: 34
Effective length of query: 467
Effective length of database: 462
Effective search space:   215754
Effective search space used:   215754
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 Sep 17 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:

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