Alignments for a candidate for HSERO_RS03640 in Pseudarthrobacter sulfonivorans Ar51

GapMind for catabolism of small carbon sources

Alignments for a candidate for HSERO_RS03640 in Pseudarthrobacter sulfonivorans Ar51

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate WP_058930145.1 AU252_RS07280 sugar ABC transporter ATP-binding protein

Query= uniprot:D8IZC7
         (521 letters)



>NCBI__GCF_001484605.1:WP_058930145.1
          Length = 506

 Score =  375 bits (963), Expect = e-108
 Identities = 205/495 (41%), Positives = 300/495 (60%), Gaps = 7/495 (1%)

Query: 5   PLLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEIL 64
           PLL++RG+ K F    AL  + L + PGE+H +MG+NGAGKSTL+K LSGVH PD GEI 
Sbjct: 9   PLLEVRGLTKRFAGVQALKGVDLQVLPGEVHCVMGQNGAGKSTLIKTLSGVHQPDGGEIR 68

Query: 65  LDGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAMRSRT 124
            +G+ + L  P A+   GI  +YQEL V   +SVA N+F+G E R+  G++      +  
Sbjct: 69  WEGKQITLPRPTAALDLGIATMYQELDVVDGLSVAENIFLGHE-RSTGGVLHVKKTNAIA 127

Query: 125 DAVLRQLGAG-FGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLF 183
             +L++LG G    S   G LS A +Q V +ARAL   ++++IMDEP+A L   E   LF
Sbjct: 128 RTLLKRLGHGSLSPSTEVGTLSAANKQIVSMARALSRDTKLIIMDEPSAILDSGEVSNLF 187

Query: 184 NVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDG-SFVGELVRDEIDSERIVQMMVGR 242
            VVR L  +G+A++YISHR+ E+  + DR++V++DG S    L   +     ++++M GR
Sbjct: 188 RVVRELTAQGIAVVYISHRLEEIRQIGDRISVIKDGRSTANGLSVTDTQKSELIRLMTGR 247

Query: 243 SLSEFYQHQRIAPADAAQLPTVMQVRALA-GGKIRPASFDVRAGEVLGFAGLVGAGRTEL 301
            ++  +  ++  PADA   P V+ V  L   G     S  VRAGE+LGFAGLVG+ R+E+
Sbjct: 248 DVANVFPERKPVPADA---PVVLDVDNLELYGHFEKVSLTVRAGEILGFAGLVGSKRSEI 304

Query: 302 ARLLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANATMN 361
              ++GA   S G + + G+ +      +A+ AGI   PE+RK QGL L   +  N T++
Sbjct: 305 LETIYGARKASSGRVSVNGKALRPGSVTSAVNAGIGLSPEERKSQGLILDEPLFKNVTLS 364

Query: 362 VASRHTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEIAPK 421
              R  R+G +   +    AR  I  L ++ A P+ P   LSGGNQQK+LLARWL     
Sbjct: 365 TFERFARMGYLNEAAERNAAREQIAALELRPADPDRPARTLSGGNQQKILLARWLVHGTS 424

Query: 422 VLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREGMITG 481
           VL+LDEPTRGVD+ A+SEIY L+ +LA  G A++V+SSE+ EV+G+ D VLV+ +G +  
Sbjct: 425 VLLLDEPTRGVDVGARSEIYDLIRKLAEAGTAIIVVSSEIEEVLGLADNVLVIDDGKVLT 484

Query: 482 ELAGAAITQENIMRL 496
           +   + I +  ++ L
Sbjct: 485 QTKASDIDEHGVLDL 499



 Score = 88.6 bits (218), Expect = 5e-22
 Identities = 63/222 (28%), Positives = 113/222 (50%), Gaps = 11/222 (4%)

Query: 27  LTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILLDGRPVALRDPGASRA--AGIN 84
           LT+R GEI    G  G+ +S +++ + G      G + ++G+  ALR    + A  AGI 
Sbjct: 283 LTVRAGEILGFAGLVGSKRSEILETIYGARKASSGRVSVNGK--ALRPGSVTSAVNAGIG 340

Query: 85  LIYQELAVAPNISVAANVFMGSELRT-----RLGLIDHAAMRSRTDAVLRQLGAGFGASD 139
           L  +E   +  + +   +F    L T     R+G ++ AA R+     +  L       D
Sbjct: 341 LSPEERK-SQGLILDEPLFKNVTLSTFERFARMGYLNEAAERNAAREQIAALELRPADPD 399

Query: 140 LAGR-LSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFNVVRRLRDEGLAIIY 198
              R LS   QQ++ +AR LVH + ++++DEPT  +      ++++++R+L + G AII 
Sbjct: 400 RPARTLSGGNQQKILLARWLVHGTSVLLLDEPTRGVDVGARSEIYDLIRKLAEAGTAIIV 459

Query: 199 ISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMV 240
           +S  + EV  LAD V V+ DG  + +    +ID   ++ +++
Sbjct: 460 VSSEIEEVLGLADNVLVIDDGKVLTQTKASDIDEHGVLDLVM 501


Lambda     K      H
   0.320    0.135    0.378 

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: 674
Number of extensions: 37
Number of successful extensions: 8
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: 521
Length of database: 506
Length adjustment: 35
Effective length of query: 486
Effective length of database: 471
Effective search space:   228906
Effective search space used:   228906
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 Apr 09 2024. 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