Alignments for a candidate for rbsA in Phyllobacterium brassicacearum STM 196

GapMind for catabolism of small carbon sources

Alignments for a candidate for rbsA in Phyllobacterium brassicacearum STM 196

Align Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (characterized)
to candidate WP_106709787.1 CU102_RS04475 sugar ABC transporter ATP-binding protein

Query= TCDB::Q9X051
         (523 letters)



>NCBI__GCF_003010955.1:WP_106709787.1
          Length = 514

 Score =  400 bits (1028), Expect = e-116
 Identities = 228/504 (45%), Positives = 326/504 (64%), Gaps = 13/504 (2%)

Query: 9   REVLLEARNITKTFPGVIAVNNVTLQIYKGEVCALVGENGAGKSTLMKILAGVYPDYEGQ 68
           RE +L  RN+TK F  V A+ NV   + +GEV AL GENGAGKSTLM I+AGV    EG+
Sbjct: 2   REPVLSIRNVTKHFGAVKALTNVNFALERGEVHALCGENGAGKSTLMNIIAGVLQPDEGE 61

Query: 69  IFLEGKEVRFRNPREAQENGIALIPQELDLVPNLSSAENIFLSREPVNEFGVIEYQKMFE 128
           I L+GK VR  +P  AQ  G+ L+ QE+ L P+ S AENIF++        ++ Y+K+  
Sbjct: 62  IVLDGKTVRIGSPAAAQSLGLGLVHQEIALCPDASVAENIFMASISRQRSLLMNYRKLER 121

Query: 129 QASKLFSKLGVNIDPKTKVEDLSTSQQQMVAIAKALSLDAKIIIMDEPTSAIGKRETEQL 188
           +A  + S+L   ID + KV +L  S QQ+V IAKAL+LD +++I DEPT+A+ + E   L
Sbjct: 122 EAQAVMSRLAP-IDVRRKVGELPISSQQLVEIAKALTLDCRVLIFDEPTAALTEAEARIL 180

Query: 189 FNIIRSLKNEGKSVIYISHRLEEIFEIADRVVVMRDGRKVGEGPIEEFDHDKLVRLMVGR 248
           F IIR LK  G S++YISHR+ EIFE+ DRV V+RDGR V    + +   D +VR MVGR
Sbjct: 181 FEIIRDLKANGISIVYISHRMAEIFELCDRVTVLRDGRYVSTDRVADLTPDDVVRRMVGR 240

Query: 249 SIDQFFIKERAT---ITDEIFRVEGIKLWSLDRKKLLVDDVSFYVRKGEVLGIYGLVGAG 305
            I Q +  ++       + +F V G+     D ++    DV   + +GE+LGI GL+G+G
Sbjct: 241 EITQLYPPKQPAGERPQEVVFSVRGLG----DNERFR--DVDIDLTRGEILGIGGLIGSG 294

Query: 306 RTELLEAIFGAHPGRTEGKVFIGGKEIKIHSPRDAVKNGIGLVPEDRKTAGLILQMSVLH 365
           RTE+ E I G     T G++ I GK+  I +  DAVK G+  + EDRK +GL L +S+  
Sbjct: 295 RTEIAEGICGLR-ATTNGQILIHGKQQAIGTYADAVKAGLVYLSEDRKGSGLFLDLSIAK 353

Query: 366 NITLPSVVMKLIVRKFGLIDSQLEKEIVRSFIEKLNIKTPSPYQIVENLSGGNQQKVVLA 425
           NI++ +  +  +    GLID+  E ++ R F ++LNI+  S    V +LSGGNQQKV +A
Sbjct: 354 NISVLN--LDALTGHLGLIDTVGEGDLARDFAQRLNIRMGSIGAPVSSLSGGNQQKVAIA 411

Query: 426 KWLAIKPKVLLLDEPTRGIDVNAKSEIYKLISEMAVSGMGVVMVSSELPEILAMSDRILV 485
           K LAI+PKV+L+DEPTRGIDV AKSEI+ L+ E+A SG+G++++SSELPE+L + DR++V
Sbjct: 412 KQLAIQPKVILMDEPTRGIDVGAKSEIHALLRELAQSGIGIIVISSELPELLGLCDRVIV 471

Query: 486 MSEGRKTAEFLREEVTEEDLLKAA 509
           + EG    E   +++TEE +++ A
Sbjct: 472 IREGEVAGELGMDDMTEERVIRLA 495



 Score = 96.3 bits (238), Expect = 2e-24
 Identities = 66/248 (26%), Positives = 121/248 (48%), Gaps = 10/248 (4%)

Query: 6   EKEREVLLEARNITKTFPGVIAVNNVTLQIYKGEVCALVGENGAGKSTLMKILAGVYPDY 65
           E+ +EV+   R +           +V + + +GE+  + G  G+G++ + + + G+    
Sbjct: 254 ERPQEVVFSVRGLGDNE----RFRDVDIDLTRGEILGIGGLIGSGRTEIAEGICGLRATT 309

Query: 66  EGQIFLEGKEVRFRNPREAQENGIALIPQELD---LVPNLSSAENIFLSREPV--NEFGV 120
            GQI + GK+       +A + G+  + ++     L  +LS A+NI +          G+
Sbjct: 310 NGQILIHGKQQAIGTYADAVKAGLVYLSEDRKGSGLFLDLSIAKNISVLNLDALTGHLGL 369

Query: 121 IEYQKMFEQASKLFSKLGVNIDP-KTKVEDLSTSQQQMVAIAKALSLDAKIIIMDEPTSA 179
           I+     + A     +L + +      V  LS   QQ VAIAK L++  K+I+MDEPT  
Sbjct: 370 IDTVGEGDLARDFAQRLNIRMGSIGAPVSSLSGGNQQKVAIAKQLAIQPKVILMDEPTRG 429

Query: 180 IGKRETEQLFNIIRSLKNEGKSVIYISHRLEEIFEIADRVVVMRDGRKVGEGPIEEFDHD 239
           I      ++  ++R L   G  +I IS  L E+  + DRV+V+R+G   GE  +++   +
Sbjct: 430 IDVGAKSEIHALLRELAQSGIGIIVISSELPELLGLCDRVIVIREGEVAGELGMDDMTEE 489

Query: 240 KLVRLMVG 247
           +++RL  G
Sbjct: 490 RVIRLASG 497



 Score = 89.7 bits (221), Expect = 2e-22
 Identities = 64/232 (27%), Positives = 121/232 (52%), Gaps = 14/232 (6%)

Query: 285 DVSFYVRKGEVLGIYGLVGAGRTELLEAIFGAHPGRTEGKVFIGGKEIKIHSPRDAVKNG 344
           +V+F + +GEV  + G  GAG++ L+  I G      EG++ + GK ++I SP  A   G
Sbjct: 23  NVNFALERGEVHALCGENGAGKSTLMNIIAGVLQP-DEGEIVLDGKTVRIGSPAAAQSLG 81

Query: 345 IGLVPEDRKTAGLILQMSVLHNITLPSVVMKLIVRKFGLIDSQLEKEI--VRSFIEKLNI 402
           +GLV ++     L    SV  NI + S+  +   R   +   +LE+E   V S +  +++
Sbjct: 82  LGLVHQE---IALCPDASVAENIFMASISRQ---RSLLMNYRKLEREAQAVMSRLAPIDV 135

Query: 403 KTPSPYQIVENLSGGNQQKVVLAKWLAIKPKVLLLDEPTRGIDVNAKSEIYKLISEMAVS 462
           +       V  L   +QQ V +AK L +  +VL+ DEPT  +       ++++I ++  +
Sbjct: 136 RRK-----VGELPISSQQLVEIAKALTLDCRVLIFDEPTAALTEAEARILFEIIRDLKAN 190

Query: 463 GMGVVMVSSELPEILAMSDRILVMSEGRKTAEFLREEVTEEDLLKAAIPRSV 514
           G+ +V +S  + EI  + DR+ V+ +GR  +     ++T +D+++  + R +
Sbjct: 191 GISIVYISHRMAEIFELCDRVTVLRDGRYVSTDRVADLTPDDVVRRMVGREI 242


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: 654
Number of extensions: 45
Number of successful extensions: 11
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 4
Number of HSP's successfully gapped: 3
Length of query: 523
Length of database: 514
Length adjustment: 35
Effective length of query: 488
Effective length of database: 479
Effective search space:   233752
Effective search space used:   233752
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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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