Alignments for a candidate for rbsA in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for rbsA in Cupriavidus basilensis 4G11

Align Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (characterized)
to candidate RR42_RS32900 RR42_RS32900 sugar ABC transporter ATPase

Query= TCDB::Q9X051
         (523 letters)



>FitnessBrowser__Cup4G11:RR42_RS32900
          Length = 502

 Score =  384 bits (987), Expect = e-111
 Identities = 221/512 (43%), Positives = 315/512 (61%), Gaps = 23/512 (4%)

Query: 3   LNTEKEREVLLEARNITKTFPGVIAVNNVTLQIYKGEVCALVGENGAGKSTLMKILAGVY 62
           +N   E   L E R I K FPGV A+++V+  IY GEV  L+GENGAGKS+LMK+L GVY
Sbjct: 1   MNAITEITPLFEMRGICKNFPGVKALDDVSFAIYPGEVHMLLGENGAGKSSLMKVLCGVY 60

Query: 63  PDYEGQIFLEGKEVRFRNPREAQENGIALIPQELDLVPNLSSAENIFLSREPVNEF-GVI 121
               G+ + +G  V   +P +    GIA+I QE  LVP L  A+NIFL REP     G +
Sbjct: 61  VADAGEFYHDGSPVAITSPADTMGLGIAVIFQEFSLVPYLDIAQNIFLGREPRGRIPGSV 120

Query: 122 EYQKMFEQASKLFSKLGVNIDPKTKVEDLSTSQQQMVAIAKALSLDAKIIIMDEPTSAIG 181
           +  +M  +A ++   LG+ +  +T V  L  +QQQMV IAKALS +A+I+++DEPT+A+ 
Sbjct: 121 DAARMHAEARRILDILGMEVSTRTPVHRLGVAQQQMVEIAKALSQNARILVLDEPTAALS 180

Query: 182 KRETEQLFNIIRSLKNEGKSVIYISHRLEEIFEIADRVVVMRDGRKVGEGPIEEFDHDKL 241
            RETE+LF +I  LK +G S+IYISHR+ E+F + DR+ ++RDGRKVG     +   D+L
Sbjct: 181 DRETEKLFAVIARLKADGVSMIYISHRMAEVFALGDRITILRDGRKVGACLPGDATPDEL 240

Query: 242 VRLMVGRSIDQFFIKERATITDEIFRVEGIKLWSLDRKKLLVD----DVSFYVRKGEVLG 297
           V  MVGR +D  + +ER+    E+         +LD + +  D    D++  VR GE++G
Sbjct: 241 VARMVGRKVDMSYSRERSAQPGEV---------ALDVRNVSADSGIADINLQVRAGEIVG 291

Query: 298 IYGLVGAGRTELLEAIFGAHPGRTEGKVFIGGKEIKIHSPRDAVKNGIGLVPEDRKTAGL 357
           + GLVG+GR+E+  A+FGA P R +G+++I GK +    P  A + G  L+PE RK+ GL
Sbjct: 292 LAGLVGSGRSEVARAVFGADPIR-QGEIYIFGKRL-TGGPDRARELGAALIPESRKSEGL 349

Query: 358 ILQMSVLHNITLPSVVMKLIVR--KFGLIDSQLEKEIVRSFIEKLNIKTPSPYQIVENLS 415
            L  +V  N+ L  +      R  +    ++  E+EI R     L I TP   Q+ + LS
Sbjct: 350 ALIRTVRDNLLLAGLRRAFPARWYRADKAEALAEREIAR-----LRIATPDGNQLAQFLS 404

Query: 416 GGNQQKVVLAKWLAIKPKVLLLDEPTRGIDVNAKSEIYKLISEMAVSGMGVVMVSSELPE 475
           GGNQQK+V+ KWL  + K+ + DEPTRGIDV AK+EI+ LI  +   G GV+++SSELPE
Sbjct: 405 GGNQQKIVIGKWLVAEAKLFIFDEPTRGIDVGAKAEIFALIDSLVKQGAGVLLISSELPE 464

Query: 476 ILAMSDRILVMSEGRKTAEFLREEVTEEDLLK 507
           I+ + DR  VM  GR   E    E+TEE +L+
Sbjct: 465 IINVCDRTYVMRGGRIAGEVAHAEMTEERILQ 496



 Score = 96.7 bits (239), Expect = 2e-24
 Identities = 72/247 (29%), Positives = 117/247 (47%), Gaps = 24/247 (9%)

Query: 10  EVLLEARNITKTFPGVIAVNNVTLQIYKGEVCALVGENGAGKSTLMKILAGVYPDYEGQI 69
           EV L+ RN++        + ++ LQ+  GE+  L G  G+G+S + + + G  P  +G+I
Sbjct: 263 EVALDVRNVSADS----GIADINLQVRAGEIVGLAGLVGSGRSEVARAVFGADPIRQGEI 318

Query: 70  FLEGKEVRFRNPREAQENGIALIPQELDLVPNLSSAENIFLSREPVNEFGVIEYQKMFEQ 129
           ++ GK +    P  A+E G ALIP+          +E + L R   +   +   ++ F  
Sbjct: 319 YIFGKRLT-GGPDRARELGAALIPES-------RKSEGLALIRTVRDNLLLAGLRRAFPA 370

Query: 130 -----------ASKLFSKLGVNI-DPKTKVEDLSTSQQQMVAIAKALSLDAKIIIMDEPT 177
                      A +  ++L +   D     + LS   QQ + I K L  +AK+ I DEPT
Sbjct: 371 RWYRADKAEALAEREIARLRIATPDGNQLAQFLSGGNQQKIVIGKWLVAEAKLFIFDEPT 430

Query: 178 SAIGKRETEQLFNIIRSLKNEGKSVIYISHRLEEIFEIADRVVVMRDGRKVGEGPIEEFD 237
             I      ++F +I SL  +G  V+ IS  L EI  + DR  VMR GR  GE    E  
Sbjct: 431 RGIDVGAKAEIFALIDSLVKQGAGVLLISSELPEIINVCDRTYVMRGGRIAGEVAHAEMT 490

Query: 238 HDKLVRL 244
            +++++L
Sbjct: 491 EERILQL 497



 Score = 92.4 bits (228), Expect = 3e-23
 Identities = 62/232 (26%), Positives = 115/232 (49%), Gaps = 8/232 (3%)

Query: 283 VDDVSFYVRKGEVLGIYGLVGAGRTELLEAIFGAHPGRTEGKVFIGGKEIKIHSPRDAVK 342
           +DDVSF +  GEV  + G  GAG++ L++ + G +     G+ +  G  + I SP D + 
Sbjct: 26  LDDVSFAIYPGEVHMLLGENGAGKSSLMKVLCGVYVADA-GEFYHDGSPVAITSPADTMG 84

Query: 343 NGIGLVPEDRKTAGLILQMSVLHNITLPSVVMKLIVRKFGLIDSQLEKEIVRSFIEKLNI 402
            GI ++ ++     L+  + +  NI L       I    G +D+       R  ++ L +
Sbjct: 85  LGIAVIFQE---FSLVPYLDIAQNIFLGREPRGRIP---GSVDAARMHAEARRILDILGM 138

Query: 403 KTPSPYQIVENLSGGNQQKVVLAKWLAIKPKVLLLDEPTRGIDVNAKSEIYKLISEMAVS 462
           +  S    V  L    QQ V +AK L+   ++L+LDEPT  +      +++ +I+ +   
Sbjct: 139 EV-STRTPVHRLGVAQQQMVEIAKALSQNARILVLDEPTAALSDRETEKLFAVIARLKAD 197

Query: 463 GMGVVMVSSELPEILAMSDRILVMSEGRKTAEFLREEVTEEDLLKAAIPRSV 514
           G+ ++ +S  + E+ A+ DRI ++ +GRK    L  + T ++L+   + R V
Sbjct: 198 GVSMIYISHRMAEVFALGDRITILRDGRKVGACLPGDATPDELVARMVGRKV 249


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: 617
Number of extensions: 31
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: 523
Length of database: 502
Length adjustment: 35
Effective length of query: 488
Effective length of database: 467
Effective search space:   227896
Effective search space used:   227896
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 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