Alignments for a candidate for BPHYT_RS16930 in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for BPHYT_RS16930 in Cupriavidus basilensis 4G11

Align Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale)
to candidate RR42_RS32900 RR42_RS32900 sugar ABC transporter ATPase

Query= uniprot:B2SYR5
         (512 letters)



>FitnessBrowser__Cup4G11:RR42_RS32900
          Length = 502

 Score =  377 bits (967), Expect = e-109
 Identities = 220/490 (44%), Positives = 305/490 (62%), Gaps = 11/490 (2%)

Query: 10  IGKVFPGVRALDGVSFDVNVGQVHGLMGENGAGKSTLLKILGGEYQPDSGRVMIDGNEVR 69
           I K FPGV+ALD VSF +  G+VH L+GENGAGKS+L+K+L G Y  D+G    DG+ V 
Sbjct: 16  ICKNFPGVKALDDVSFAIYPGEVHMLLGENGAGKSSLMKVLCGVYVADAGEFYHDGSPVA 75

Query: 70  FTSAASSIAAGIAVIHQELQYVPDLTVAENLLLGQLPNSL--GWVNKREAKRFVRERLEA 127
            TS A ++  GIAVI QE   VP L +A+N+ LG+ P     G V+        R  L+ 
Sbjct: 76  ITSPADTMGLGIAVIFQEFSLVPYLDIAQNIFLGREPRGRIPGSVDAARMHAEARRILDI 135

Query: 128 MGVALDPNAKLRKLSIAQRQMVEICKALLRNARVIALDEPTSSLSHRETEVLFKLVRDLR 187
           +G+ +     + +L +AQ+QMVEI KAL +NAR++ LDEPT++LS RETE LF ++  L+
Sbjct: 136 LGMEVSTRTPVHRLGVAQQQMVEIAKALSQNARILVLDEPTAALSDRETEKLFAVIARLK 195

Query: 188 ADNRAMIYISHRMDEIYELCDACTIFRDGRKIASHPTLEG-VTRDTIVSEMVGREISDIY 246
           AD  +MIYISHRM E++ L D  TI RDGRK+ +   L G  T D +V+ MVGR++   Y
Sbjct: 196 ADGVSMIYISHRMAEVFALGDRITILRDGRKVGA--CLPGDATPDELVARMVGRKVDMSY 253

Query: 247 N--YSARPLGEVRFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELMHLVYGADH 304
           +   SA+P GEV    + +   +     + +VR GEIVG  GLVG+GRSE+   V+GAD 
Sbjct: 254 SRERSAQP-GEVALDVRNVSADSGIADINLQVRAGEIVGLAGLVGSGRSEVARAVFGADP 312

Query: 305 KKGGELLLDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCRRHYLRVG 364
            + GE+ + GK +       A   G  L PE RK EG+  + TV +N+ ++  R      
Sbjct: 313 IRQGEIYIFGKRL-TGGPDRARELGAALIPESRKSEGLALIRTVRDNLLLAGLRRAFPAR 371

Query: 365 MFLDRKKEAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWLAEPDLKVVILDEP 424
            +   K EA  A+R I  L+I TP   Q  +FLSGGNQQK ++ +WL   + K+ I DEP
Sbjct: 372 WYRADKAEA-LAEREIARLRIATPDGNQLAQFLSGGNQQKIVIGKWLV-AEAKLFIFDEP 429

Query: 425 TRGIDVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRISGELTRKDA 484
           TRGIDVGAK EI+ +I  L ++G  +++ISSELPE++ V DR  VMR GRI+GE+   + 
Sbjct: 430 TRGIDVGAKAEIFALIDSLVKQGAGVLLISSELPEIINVCDRTYVMRGGRIAGEVAHAEM 489

Query: 485 TEQSVLSLAL 494
           TE+ +L L +
Sbjct: 490 TEERILQLGM 499



 Score = 89.4 bits (220), Expect = 3e-22
 Identities = 65/240 (27%), Positives = 115/240 (47%), Gaps = 6/240 (2%)

Query: 252 PLGEVRFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELMHLVYGADHKKGGELL 311
           PL E+R   K   G       SF +  GE+    G  GAG+S LM ++ G      GE  
Sbjct: 9   PLFEMRGICKNFPGVKALDDVSFAIYPGEVHMLLGENGAGKSSLMKVLCGVYVADAGEFY 68

Query: 312 LDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCRRHYLRVGMFLDRKK 371
            DG P+ + S  + +  GI +     +E  +V    +++NI +  R    R+   +D  +
Sbjct: 69  HDGSPVAITSPADTMGLGIAVI---FQEFSLVPYLDIAQNIFLG-REPRGRIPGSVDAAR 124

Query: 372 EAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWLAEPDLKVVILDEPTRGIDVG 431
               A R + +L ++  S R  +  L    QQ   +++ L++ + ++++LDEPT  +   
Sbjct: 125 MHAEARRILDILGMEV-STRTPVHRLGVAQQQMVEIAKALSQ-NARILVLDEPTAALSDR 182

Query: 432 AKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRISGELTRKDATEQSVLS 491
              +++ VI +L   G +++ IS  + EV  + DRI ++R GR  G     DAT   +++
Sbjct: 183 ETEKLFAVIARLKADGVSMIYISHRMAEVFALGDRITILRDGRKVGACLPGDATPDELVA 242


Lambda     K      H
   0.320    0.136    0.385 

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: 648
Number of extensions: 29
Number of successful extensions: 10
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: 512
Length of database: 502
Length adjustment: 34
Effective length of query: 478
Effective length of database: 468
Effective search space:   223704
Effective search space used:   223704
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: 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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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