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 ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate Ac3H11_1841 Ribose ABC transport system, ATP-binding protein RbsA (TC 3.A.1.2.1)

Query= uniprot:D8IUD1
         (522 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1841
          Length = 892

 Score =  420 bits (1080), Expect = e-121
 Identities = 234/446 (52%), Positives = 288/446 (64%), Gaps = 34/446 (7%)

Query: 1   MQPNDSLSQGSPLLTLSGIGKRYAAPVLDGIDLDLRPGQVLALTGENGAGKSTLSKIICG 60
           M P    +   PLL +  IGK Y A VLDG++++L  G+VLALTGENGAGKSTLSKI+CG
Sbjct: 10  MTPKPPTNTSPPLLAIQAIGKDYTATVLDGVNVELFAGEVLALTGENGAGKSTLSKILCG 69

Query: 61  LVDASAGGMMLDGQPYAPASRTQAEGLGIRMVMQELNLIPTLSIAENLFLEKLPRRFGWI 120
           L   + GGM+L GQ YAP SR  AE  G+RMVMQEL L+PTL++AENL + +LP R GW+
Sbjct: 70  LEQPTRGGMLLAGQAYAPTSRRDAERHGVRMVMQELGLVPTLTVAENLLMGRLPHRLGWL 129

Query: 121 DRKKLAEAARAQMEVVGLGELDPWTPVGDLGLGHQQMVEIARNLIGSCRCLILDEPTAML 180
            R  L  AARAQ+  +GL  +DP TPV  LG+G QQMVEIARNL    R L+LDEPTAML
Sbjct: 130 QRDVLHAAARAQLAKIGLDSIDPATPVSQLGIGQQQMVEIARNLQDDTRILVLDEPTAML 189

Query: 181 TNREVELLFSRIERLRAEGVAIIYISHRLEELKRIADRIVVLRDGKLVCNDDIGRYSTEQ 240
           T RE   LF +I  L A GVAIIY+SHRLEEL+RIADR+ VLRDG+LV    +   S + 
Sbjct: 190 TPRETNYLFEQIAHLTARGVAIIYVSHRLEELRRIADRVAVLRDGRLVDVRPMAGMSEDD 249

Query: 241 LVQLMAGELTKVDLDAEHRR-IGAPVLRIRGLGRAPVVHPASLALHAGEVLGIAGLIGSG 299
           LVQ M G +   DLD   RR +G  V+   GLGR   V   SL L AGE+ GIAGL+GSG
Sbjct: 250 LVQRMVGRVVS-DLDHRPRRPVGPVVMSAEGLGRGTAVQGVSLELRAGEIFGIAGLVGSG 308

Query: 300 RTELLRLIFGADRAEQGEIFI-----------GDSQEPARIR------------------ 330
           RTEL+RL+FGADRA++G + +            D Q  A I+                  
Sbjct: 309 RTELVRLLFGADRADRGSVTLHPEFEQKQALPRDGQAQAAIQKIANTPNPATAAPRTWQR 368

Query: 331 ---SPKDAVKAGIAMVTEDRKGQGLLLPQAISVNTSLANLGSVSRGGMLDHAAESSVAQD 387
              SP  A+ AG+ +VTEDRK QGLLL Q I +N +L++L +VSRGG L    E+ + Q 
Sbjct: 369 GFASPLQAIAAGVGLVTEDRKSQGLLLSQPIRINATLSDLSAVSRGGWLQRGFENRLVQG 428

Query: 388 YVKKLRIRSGSVAQAAGELSGGNQQK 413
           +V+ L IR  S  Q  G+LSGGNQQK
Sbjct: 429 FVRTLGIRCRSPEQPVGQLSGGNQQK 454



 Score = 94.4 bits (233), Expect = 2e-23
 Identities = 73/243 (30%), Positives = 122/243 (50%), Gaps = 17/243 (6%)

Query: 264 PVLRIRGLGR---APVVHPASLALHAGEVLGIAGLIGSGRTELLRLIFGADRAEQGEIFI 320
           P+L I+ +G+   A V+   ++ L AGEVL + G  G+G++ L +++ G ++  +G + +
Sbjct: 21  PLLAIQAIGKDYTATVLDGVNVELFAGEVLALTGENGAGKSTLSKILCGLEQPTRGGMLL 80

Query: 321 -GDSQEPARIRSPKDAVKAGIAMVTEDRKGQGLLLPQAISVNTSLANLGSVSRGGMLDHA 379
            G +  P    S +DA + G+ MV ++    GL+    ++ N  +  L    R G L   
Sbjct: 81  AGQAYAPT---SRRDAERHGVRMVMQEL---GLVPTLTVAENLLMGRLPH--RLGWLQRD 132

Query: 380 AESSVAQDYVKKLRIRSGSVAQAAGELSGGNQQKVVIARWLYRDCPIMLFDEPTRGIDIG 439
              + A+  + K+ + S   A    +L  G QQ V IAR L  D  I++ DEPT  +   
Sbjct: 133 VLHAAARAQLAKIGLDSIDPATPVSQLGIGQQQMVEIARNLQDDTRILVLDEPTAMLTPR 192

Query: 440 AKSDIYRLFAELAAQGKGLLVVSSDLRELMQICDRIAVMSAGRIADT-----FSRDDWSQ 494
             + ++   A L A+G  ++ VS  L EL +I DR+AV+  GR+ D       S DD  Q
Sbjct: 193 ETNYLFEQIAHLTARGVAIIYVSHRLEELRRIADRVAVLRDGRLVDVRPMAGMSEDDLVQ 252

Query: 495 ERI 497
             +
Sbjct: 253 RMV 255


Lambda     K      H
   0.320    0.137    0.390 

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: 1194
Number of extensions: 71
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: 522
Length of database: 892
Length adjustment: 39
Effective length of query: 483
Effective length of database: 853
Effective search space:   411999
Effective search space used:   411999
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 54 (25.4 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
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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 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