Alignments for a candidate for rbsA in Rhodobacter viridis JA737

GapMind for catabolism of small carbon sources

Alignments for a candidate for rbsA in Rhodobacter viridis JA737

Align Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (characterized)
to candidate WP_110805879.1 C8J30_RS10885 sugar ABC transporter ATP-binding protein

Query= TCDB::Q9X051
         (523 letters)



>NCBI__GCF_003217355.1:WP_110805879.1
          Length = 511

 Score =  378 bits (971), Expect = e-109
 Identities = 216/491 (43%), Positives = 300/491 (61%), Gaps = 6/491 (1%)

Query: 5   TEKEREVLLEARNITKTFPGVIAVNNVTLQIYKGEVCALVGENGAGKSTLMKILAGVYPD 64
           TEK   + L  R   K +PG  A+  V   +  G V  LVGENGAGKSTLMK++AGV   
Sbjct: 2   TEKH-PIGLSIRGGVKVYPGTRALKGVDFDLRMGAVNVLVGENGAGKSTLMKLIAGVEDM 60

Query: 65  YEGQIFLEGKEVRFRNPREAQENGIALIPQELDLVPNLSSAENIFLSREPVNEFGVIEYQ 124
            EG I ++G+E+RFR   +A   GI ++ QEL+L PNLS AENIF+  E       I+ +
Sbjct: 61  TEGTITMDGREMRFRTKADAVAAGIGIVFQELNLFPNLSVAENIFIGHETTRGGIDIDIE 120

Query: 125 KMFEQASKLFSKLGVNIDPKTKVEDLSTSQQQMVAIAKALSLDAKIIIMDEPTSAIGKRE 184
              E   +L  +L  NI P T + +L   QQQ+V IAKAL+ +A+I+I+DEPTSA+   E
Sbjct: 121 AHREATRQLMERLEQNIHPDTPLGNLRIGQQQIVEIAKALAQNARILILDEPTSALSAAE 180

Query: 185 TEQLFNIIRSLKNEGKSVIYISHRLEEIFEIADRVVVMRDGRKVGEGPIEEFDHDKLVRL 244
            E LF +I  L  +G  ++YISHRLEE+  + D + V+RDG   G   +E  D   +V+ 
Sbjct: 181 VEVLFRVIDELTAQGVGIVYISHRLEELIRVGDYITVLRDGVITGARSMEGVDIPWIVKA 240

Query: 245 MVGRSIDQFFIKERATITDEIFRVEGIKLWSLDRKKLLVDDVSFYVRKGEVLGIYGLVGA 304
           M+G S  ++   E A    EIFR E I L         VD VS  +R GE++G+YGL+GA
Sbjct: 241 MIGSSSKEYGRSEVANFGPEIFRAEDITL-PRAGGGFTVDHVSLSIRSGEIVGLYGLMGA 299

Query: 305 GRTELLEAIFGAHPGRTEGKVFIGGKEIKIHSPRDAVKNGIGLVPEDRKTAGLILQMSVL 364
           GR+E LE +   HP  + GK ++ GK +        +  GI L+PEDRK  GLI  MS+ 
Sbjct: 300 GRSEFLECVMAQHP-HSGGKFWVEGKPLTERDVPGRIARGIALIPEDRKRDGLIQIMSIR 358

Query: 365 HNITLPSVVMKLIVRKFGLIDSQLEKEIVRSFIEKLNIKTPSPYQIVENLSGGNQQKVVL 424
            N+TL S+       K   +D + E +    FI++L IK  SP   V +LSGGNQQKVV+
Sbjct: 359 ENLTLSSLPS---FTKLFHLDLKKEAKTAVEFIKRLTIKVASPENPVSSLSGGNQQKVVI 415

Query: 425 AKWLAIKPKVLLLDEPTRGIDVNAKSEIYKLISEMAVSGMGVVMVSSELPEILAMSDRIL 484
            K L   PKVLL+DEP+RGID+ AK+E+++ +  +A  G+G++ V+S+L E+LA+SDRI+
Sbjct: 416 GKALMTGPKVLLMDEPSRGIDIGAKAEVFRTMRRLAAEGLGILFVTSDLDEVLALSDRII 475

Query: 485 VMSEGRKTAEF 495
           VM++GR T EF
Sbjct: 476 VMAQGRVTGEF 486



 Score =  112 bits (280), Expect = 3e-29
 Identities = 68/214 (31%), Positives = 115/214 (53%), Gaps = 5/214 (2%)

Query: 24  GVIAVNNVTLQIYKGEVCALVGENGAGKSTLMKILAGVYPDYEGQIFLEGKEVRFRNPRE 83
           G   V++V+L I  GE+  L G  GAG+S  ++ +   +P   G+ ++EGK +  R+   
Sbjct: 274 GGFTVDHVSLSIRSGEIVGLYGLMGAGRSEFLECVMAQHPHSGGKFWVEGKPLTERDVPG 333

Query: 84  AQENGIALIPQELD---LVPNLSSAENIFLSREP-VNEFGVIEYQKMFEQASKLFSKLGV 139
               GIALIP++     L+  +S  EN+ LS  P   +   ++ +K  + A +   +L +
Sbjct: 334 RIARGIALIPEDRKRDGLIQIMSIRENLTLSSLPSFTKLFHLDLKKEAKTAVEFIKRLTI 393

Query: 140 NI-DPKTKVEDLSTSQQQMVAIAKALSLDAKIIIMDEPTSAIGKRETEQLFNIIRSLKNE 198
            +  P+  V  LS   QQ V I KAL    K+++MDEP+  I      ++F  +R L  E
Sbjct: 394 KVASPENPVSSLSGGNQQKVVIGKALMTGPKVLLMDEPSRGIDIGAKAEVFRTMRRLAAE 453

Query: 199 GKSVIYISHRLEEIFEIADRVVVMRDGRKVGEGP 232
           G  +++++  L+E+  ++DR++VM  GR  GE P
Sbjct: 454 GLGILFVTSDLDEVLALSDRIIVMAQGRVTGEFP 487



 Score = 99.0 bits (245), Expect = 4e-25
 Identities = 74/232 (31%), Positives = 119/232 (51%), Gaps = 13/232 (5%)

Query: 286 VSFYVRKGEVLGIYGLVGAGRTELLEAIFGAHPGRTEGKVFIGGKEIKIHSPRDAVKNGI 345
           V F +R G V  + G  GAG++ L++ I G     TEG + + G+E++  +  DAV  GI
Sbjct: 27  VDFDLRMGAVNVLVGENGAGKSTLMKLIAGVED-MTEGTITMDGREMRFRTKADAVAAGI 85

Query: 346 GLVPEDRKTAGLILQMSVLHNITLPSVVMKLIVRKFGLIDSQLEKEIVRSFIEKL--NIK 403
           G+V ++     L   +SV  NI +     +  +     ID +  +E  R  +E+L  NI 
Sbjct: 86  GIVFQE---LNLFPNLSVAENIFIGHETTRGGID----IDIEAHREATRQLMERLEQNIH 138

Query: 404 TPSPYQIVENLSGGNQQKVVLAKWLAIKPKVLLLDEPTRGIDVNAKSEIYKLISEMAVSG 463
             +P   + NL  G QQ V +AK LA   ++L+LDEPT  +       ++++I E+   G
Sbjct: 139 PDTP---LGNLRIGQQQIVEIAKALAQNARILILDEPTSALSAAEVEVLFRVIDELTAQG 195

Query: 464 MGVVMVSSELPEILAMSDRILVMSEGRKTAEFLREEVTEEDLLKAAIPRSVK 515
           +G+V +S  L E++ + D I V+ +G  T     E V    ++KA I  S K
Sbjct: 196 VGIVYISHRLEELIRVGDYITVLRDGVITGARSMEGVDIPWIVKAMIGSSSK 247


Lambda     K      H
   0.317    0.137    0.372 

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: 638
Number of extensions: 37
Number of successful extensions: 8
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: 523
Length of database: 511
Length adjustment: 35
Effective length of query: 488
Effective length of database: 476
Effective search space:   232288
Effective search space used:   232288
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 (21.6 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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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