Alignments for a candidate for rbsA in Pseudovibrio axinellae Ad2

GapMind for catabolism of small carbon sources

Alignments for a candidate for rbsA in Pseudovibrio axinellae Ad2

Align ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 (characterized)
to candidate WP_068009665.1 PsAD2_RS19320 ATP-binding cassette domain-containing protein

Query= CharProtDB::CH_003578
         (501 letters)



>NCBI__GCF_001623255.1:WP_068009665.1
          Length = 497

 Score =  530 bits (1364), Expect = e-155
 Identities = 265/492 (53%), Positives = 352/492 (71%), Gaps = 1/492 (0%)

Query: 1   MEALLQLKGIDKAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGT 60
           M  LL+L+GI+K+F G+  L    L +  GRV+AL GENGAGKST+MK+++GIY RDAGT
Sbjct: 1   MTTLLELQGIEKSFSGINVLKSVDLTIRAGRVVALAGENGAGKSTLMKIISGIYQRDAGT 60

Query: 61  LLWLGKETTFTGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREFVNRFGKIDWKTMYA 120
           + + G E  FT  + S +AGIGIIHQELNL+P L++AENI+LGRE   + GKI W  +  
Sbjct: 61  VFYKGHEVEFTNARESMDAGIGIIHQELNLLPDLSVAENIYLGRE-PTKLGKIQWDVVQR 119

Query: 121 EADKLLAKLNLRFKSDKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESL 180
           E+ K LA+L         +G LSI  QQMVEIAK LS  ++VIIMDEPTDALTD ET  L
Sbjct: 120 ESKKYLAQLKQDIDPTTPLGKLSIAQQQMVEIAKALSLNAEVIIMDEPTDALTDIETAIL 179

Query: 181 FRVIRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTEDSLIEMMVGR 240
           F V+ EL++QG+G+V+ISHR+ EIF++CDD+ + RDGQ + +  VA ++ED LI  MVGR
Sbjct: 180 FEVVDELRAQGKGLVFISHRLGEIFQMCDDIAILRDGQMVHQGAVADISEDDLIRHMVGR 239

Query: 241 KLEDQYPHLDKAPGDIRLKVDNLCGPGVNDVSFTLRKGEILGVSGLMGAGRTELMKVLYG 300
           +L DQYP +   PGD+R++VD L   G  ++SFT   GE++G +GL+GAGRTEL K ++G
Sbjct: 240 ELSDQYPFVPAEPGDVRIEVDKLTARGAKEISFTANAGEVVGFAGLVGAGRTELAKAIFG 299

Query: 301 ALPRTSGYVTLDGHEVVTRSPQDGLANGIVYISEDRKRDGLVLGMSVKENMSLTALRYFS 360
           A P   G V +DG E+  +SPQDG+   I Y++EDRK++GLV   S+  NMSLT L  F 
Sbjct: 300 ANPIRGGSVKIDGQEISLKSPQDGVKAKIGYVTEDRKQEGLVQSQSLGSNMSLTGLDRFC 359

Query: 361 RAGGSLKHADEQQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAIARGLMTRPKVLILD 420
              G +    E   +S++I  F +KT      I  LSGGNQQKV+IA+ L+  P+VLILD
Sbjct: 360 NTLGIVNKTSEAVTISEYIEAFAIKTRDASTIISNLSGGNQQKVSIAKSLVPEPEVLILD 419

Query: 421 EPTRGVDVGAKKEIYQLINQFKADGLSIILVSSEMPEVLGMSDRIIVMHEGHLSGEFTRE 480
           EPTRGVDVGAK+EIY LIN+ KA+GL I+L+SS+MPE+LG+SDRI+V+ +G L+G F R+
Sbjct: 420 EPTRGVDVGAKREIYTLINKLKAEGLCILLISSDMPELLGISDRILVLSDGKLTGSFDRD 479

Query: 481 QATQEVLMAAAV 492
           +ATQE +M  AV
Sbjct: 480 EATQENIMRCAV 491



 Score = 85.1 bits (209), Expect = 5e-21
 Identities = 58/227 (25%), Positives = 115/227 (50%), Gaps = 7/227 (3%)

Query: 268 VNDVSFTLRKGEILGVSGLMGAGRTELMKVLYGALPRTSGYVTLDGHEVVTRSPQDGLAN 327
           +  V  T+R G ++ ++G  GAG++ LMK++ G   R +G V   GHEV   + ++ +  
Sbjct: 20  LKSVDLTIRAGRVVALAGENGAGKSTLMKIISGIYQRDAGTVFYKGHEVEFTNARESMDA 79

Query: 328 GIVYISEDRKRDGLVLGMSVKENMSLTALRYFSRAGGSLKHADEQQAVSDFIRLFNVKTP 387
           GI  I ++     L+  +SV EN+ L   R  ++ G       ++++     +L     P
Sbjct: 80  GIGIIHQELN---LLPDLSVAENIYLG--REPTKLGKIQWDVVQRESKKYLAQLKQDIDP 134

Query: 388 SMEQAIGLLSGGNQQKVAIARGLMTRPKVLILDEPTRGVDVGAKKEIYQLINQFKADGLS 447
           +    +G LS   QQ V IA+ L    +V+I+DEPT  +       +++++++ +A G  
Sbjct: 135 TTP--LGKLSIAQQQMVEIAKALSLNAEVIIMDEPTDALTDIETAILFEVVDELRAQGKG 192

Query: 448 IILVSSEMPEVLGMSDRIIVMHEGHLSGEFTREQATQEVLMAAAVGK 494
           ++ +S  + E+  M D I ++ +G +  +      +++ L+   VG+
Sbjct: 193 LVFISHRLGEIFQMCDDIAILRDGQMVHQGAVADISEDDLIRHMVGR 239


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: 710
Number of extensions: 30
Number of successful extensions: 6
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: 497
Length adjustment: 34
Effective length of query: 467
Effective length of database: 463
Effective search space:   216221
Effective search space used:   216221
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 24 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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