Alignments for a candidate for BPHYT_RS34245 in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for BPHYT_RS34245 in Cupriavidus basilensis 4G11

Align ABC transporter related; Flags: Precursor (characterized, see rationale)
to candidate RR42_RS32900 RR42_RS32900 sugar ABC transporter ATPase

Query= uniprot:B2T9V9
         (510 letters)



>FitnessBrowser__Cup4G11:RR42_RS32900
          Length = 502

 Score =  264 bits (674), Expect = 6e-75
 Identities = 164/490 (33%), Positives = 265/490 (54%), Gaps = 13/490 (2%)

Query: 5   MSELTSSVPVVEALEVTKRFGSTAALNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLR 64
           M+ +T   P+ E   + K F    AL+DVS  + PGE H L+G NGAGKS+L+ +L G+ 
Sbjct: 1   MNAITEITPLFEMRGICKNFPGVKALDDVSFAIYPGEVHMLLGENGAGKSSLMKVLCGVY 60

Query: 65  KPDTGEVRFSGAAAPSIADRDAWRERVACVYQHSTIIRDLSVAENLFINRQPLRG---GV 121
             D GE    G+     +  D     +A ++Q  +++  L +A+N+F+ R+P RG   G 
Sbjct: 61  VADAGEFYHDGSPVAITSPADTMGLGIAVIFQEFSLVPYLDIAQNIFLGREP-RGRIPGS 119

Query: 122 IDWQAMRRDARALLDHWKIDVREDARAGDLSVEARQLVEIARALSYGARFIILDEPTAQL 181
           +D   M  +AR +LD   ++V        L V  +Q+VEIA+ALS  AR ++LDEPTA L
Sbjct: 120 VDAARMHAEARRILDILGMEVSTRTPVHRLGVAQQQMVEIAKALSQNARILVLDEPTAAL 179

Query: 182 DGDEIKRLFRRISELQREGVTFLFISHHLQEVYEICQAVTVLRDARHI-VSAPVSALPRE 240
              E ++LF  I+ L+ +GV+ ++ISH + EV+ +   +T+LRD R +    P  A P +
Sbjct: 180 SDRETEKLFAVIARLKADGVSMIYISHRMAEVFALGDRITILRDGRKVGACLPGDATP-D 238

Query: 241 QLIEAMTGERGGLAVADAAARGALPADTAVALELKELTG-ADYEGVSFTVKRGEVVGLTG 299
           +L+  M G +  + ++ +  R A P +  VAL+++ ++  +    ++  V+ GE+VGL G
Sbjct: 239 ELVARMVGRK--VDMSYSRERSAQPGE--VALDVRNVSADSGIADINLQVRAGEIVGLAG 294

Query: 300 ATSSGRTSVAEAIAGLRAAKRGTISVDGAILPPGDVPASLAHGIGCVPKDRHHEGLVLTQ 359
              SGR+ VA A+ G    ++G I + G  L  G   A    G   +P+ R  EGL L +
Sbjct: 295 LVGSGRSEVARAVFGADPIRQGEIYIFGKRLTGGPDRAR-ELGAALIPESRKSEGLALIR 353

Query: 360 SVAENASMTIARVLGKFGIAAPAKKNAFGQKMIDALGIVAQGPEHVVSGLSGGNQQKVVM 419
           +V +N  +   R           K  A  ++ I  L I       +   LSGGNQQK+V+
Sbjct: 354 TVRDNLLLAGLRRAFPARWYRADKAEALAEREIARLRIATPDGNQLAQFLSGGNQQKIVI 413

Query: 420 ARALATNPNVLVLIDPTAGVDVKSKEALLSVVDRVREEGKAVLVVSGELDD-LRTCDRVL 478
            + L     + +  +PT G+DV +K  + +++D + ++G  VL++S EL + +  CDR  
Sbjct: 414 GKWLVAEAKLFIFDEPTRGIDVGAKAEIFALIDSLVKQGAGVLLISSELPEIINVCDRTY 473

Query: 479 VMFRGRVAAE 488
           VM  GR+A E
Sbjct: 474 VMRGGRIAGE 483



 Score = 53.9 bits (128), Expect = 1e-11
 Identities = 58/242 (23%), Positives = 103/242 (42%), Gaps = 10/242 (4%)

Query: 10  SSVPVVEALEVTKRFGSTAALNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPDTG 69
           S+ P   AL+V +   + + + D++++V  GE   L G  G+G+S +   + G      G
Sbjct: 258 SAQPGEVALDV-RNVSADSGIADINLQVRAGEIVGLAGLVGSGRSEVARAVFGADPIRQG 316

Query: 70  EVRFSGAAAPSIADRDAWRERVACVYQHSTIIRDLS----VAENLFINRQPLRGGVIDWQ 125
           E+   G       DR   RE  A +   S     L+    V +NL +           ++
Sbjct: 317 EIYIFGKRLTGGPDRA--RELGAALIPESRKSEGLALIRTVRDNLLLAGLRRAFPARWYR 374

Query: 126 AMRRDARALLDHWKIDVRE---DARAGDLSVEARQLVEIARALSYGARFIILDEPTAQLD 182
           A + +A A  +  ++ +     +  A  LS   +Q + I + L   A+  I DEPT  +D
Sbjct: 375 ADKAEALAEREIARLRIATPDGNQLAQFLSGGNQQKIVIGKWLVAEAKLFIFDEPTRGID 434

Query: 183 GDEIKRLFRRISELQREGVTFLFISHHLQEVYEICQAVTVLRDARHIVSAPVSALPREQL 242
                 +F  I  L ++G   L IS  L E+  +C    V+R  R       + +  E++
Sbjct: 435 VGAKAEIFALIDSLVKQGAGVLLISSELPEIINVCDRTYVMRGGRIAGEVAHAEMTEERI 494

Query: 243 IE 244
           ++
Sbjct: 495 LQ 496


Lambda     K      H
   0.318    0.134    0.377 

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: 568
Number of extensions: 32
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: 510
Length of database: 502
Length adjustment: 34
Effective length of query: 476
Effective length of database: 468
Effective search space:   222768
Effective search space used:   222768
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 (21.7 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