Alignments for a candidate for HSERO_RS03640 in Stutzerimonas stutzeri A1501

GapMind for catabolism of small carbon sources

Alignments for a candidate for HSERO_RS03640 in Stutzerimonas stutzeri A1501

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate WP_011914604.1 PST_RS17845 ABC transporter ATP-binding protein

Query= uniprot:D8IZC7
         (521 letters)



>NCBI__GCF_000013785.1:WP_011914604.1
          Length = 525

 Score =  248 bits (633), Expect = 4e-70
 Identities = 165/501 (32%), Positives = 258/501 (51%), Gaps = 28/501 (5%)

Query: 1   MTQTPLLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQ 60
           M+    +Q+ G+ KSF   +ALS    T R GE+HAL+GENGAGKS+LM + +G++AP+ 
Sbjct: 1   MSNLNAIQLSGVSKSFDGFMALSQADFTARWGEVHALLGENGAGKSSLMNIAAGLYAPES 60

Query: 61  GEILLDGRPVALRDPGASRAAGINLIYQELAVAPNISVAANV------------FMGSEL 108
           G +L++   V L  P  +    I +++Q   +    +VA N+            F GS  
Sbjct: 61  GSLLINDNAVRLSGPRDASRYHIGMVHQHFKLVKPFTVAENIQLALPEGPGNHAFSGSH- 119

Query: 109 RTRLGLIDHAAMRSRTDAVLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMD 168
           R RL     AA+  R      +LG       +   LS+AEQQ+VEI + L+  +RI+I+D
Sbjct: 120 RQRL-----AALEQRISDKAAELGFSIDPRKITESLSVAEQQRVEILKVLLAGARILILD 174

Query: 169 EPTAALSERETEQLFNVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRD 228
           EPTA L++ E E+L   VR    +G A+I ++H+M++V   ADRVTV+R G  +  L   
Sbjct: 175 EPTAVLTDGEAERLLETVRAFARQGAAVILVTHKMSDVKRFADRVTVMRGGRTIQTLDPQ 234

Query: 229 EIDSERIVQMMVGRSLSEFYQHQRIAPADAAQLPTVMQVRALAGGKIRPASFDVRAGEVL 288
            +    +V++ VG S         I      Q+  +    A   G +   +  +RAGE+ 
Sbjct: 235 TVSVPELVRLTVGESAPASEYQPAIPGEVRLQVRDLRSTGAGGQGVLNGVNLSLRAGEIY 294

Query: 289 GFAGLVGAGRTELARLLFGADPRSGGDILLEG----RPVHIDQPRAAMRAGIAYVPEDRK 344
           G AG+ G G++ELA +L G      G + L G    R    +Q R      IA +P DR 
Sbjct: 295 GIAGVGGNGQSELANVLMGLPEPCDGTLELTGFGDLRRASAEQRR---ELRIAAIPADRY 351

Query: 345 GQGLFLQMAVAANATMNV--ASRHTRLGLVRSRSLGGVARAAIQRLNVK-VAHPETPVGK 401
           G  L  +++VA N  +    + R+     +R + L   A  A+   +V+ V   +     
Sbjct: 352 GAALAGELSVAENFGVGQVHSGRYGSFFRLRRKRLEAEAAEAVAGFDVQGVRSLKQKAAL 411

Query: 402 LSGGNQQKVLLARWLEIAPKVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSEL 461
           LSGGN QK+++AR     P ++++  P+RG+D+ A + ++  +      G AV+VIS +L
Sbjct: 412 LSGGNAQKLVIAREFSRDPLLVLVHSPSRGLDVRATAAVHARLRAAREAGAAVLVISEDL 471

Query: 462 PEVIGICDRVLVMREGMITGE 482
            EV+ + DR+ VM  G I  E
Sbjct: 472 DEVLALADRIGVMSGGRIVAE 492



 Score = 85.5 bits (210), Expect = 4e-21
 Identities = 76/245 (31%), Positives = 111/245 (45%), Gaps = 13/245 (5%)

Query: 7   LQMRGIRKS-FGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILL 65
           LQ+R +R +  G    L+ ++L++R GEI+ + G  G G+S L  VL G+  P  G + L
Sbjct: 265 LQVRDLRSTGAGGQGVLNGVNLSLRAGEIYGIAGVGGNGQSELANVLMGLPEPCDGTLEL 324

Query: 66  DG----RPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAMR 121
            G    R  +       R A I       A+A  +SVA N  +G     R G       R
Sbjct: 325 TGFGDLRRASAEQRRELRIAAIPADRYGAALAGELSVAENFGVGQVHSGRYGSF-FRLRR 383

Query: 122 SRTDAVLRQLGAGFGASDL------AGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALS 175
            R +A   +  AGF    +      A  LS    Q++ IAR       +V++  P+  L 
Sbjct: 384 KRLEAEAAEAVAGFDVQGVRSLKQKAALLSGGNAQKLVIAREFSRDPLLVLVHSPSRGLD 443

Query: 176 ERETEQLFNVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERI 235
            R T  +   +R  R+ G A++ IS  + EV ALADR+ V+  G  V E  R   D + I
Sbjct: 444 VRATAAVHARLRAAREAGAAVLVISEDLDEVLALADRIGVMSGGRIVAEFDR-PADRQAI 502

Query: 236 VQMMV 240
              MV
Sbjct: 503 GSAMV 507



 Score = 79.3 bits (194), Expect = 3e-19
 Identities = 72/245 (29%), Positives = 103/245 (42%), Gaps = 21/245 (8%)

Query: 278 ASFDVRAGEVLGFAGLVGAGRTELARLLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIA 337
           A F  R GEV    G  GAG++ L  +  G      G +L+    V +  PR A R  I 
Sbjct: 25  ADFTARWGEVHALLGENGAGKSSLMNIAAGLYAPESGSLLINDNAVRLSGPRDASRYHIG 84

Query: 338 YVPEDRKGQGLFLQMAVAANATMNVAS---RHTRLGLVRSRSLGGVARAAIQRLNVKVAH 394
            V +  K   L     VA N  + +      H   G  R R       A  QR++ K A 
Sbjct: 85  MVHQHFK---LVKPFTVAENIQLALPEGPGNHAFSGSHRQR-----LAALEQRISDKAAE 136

Query: 395 ------PETPVGKLSGGNQQKVLLARWLEIAPKVLILDEPTRGVDIYAKSEIYQLVHRLA 448
                 P      LS   QQ+V + + L    ++LILDEPT  +       + + V   A
Sbjct: 137 LGFSIDPRKITESLSVAEQQRVEILKVLLAGARILILDEPTAVLTDGEAERLLETVRAFA 196

Query: 449 SQGVAVVVISSELPEVIGICDRVLVMREGMITGELAGAAITQENIMRLATDTNVPRTAPA 508
            QG AV++++ ++ +V    DRV VMR G     L    ++   ++RL     V  +APA
Sbjct: 197 RQGAAVILVTHKMSDVKRFADRVTVMRGGRTIQTLDPQTVSVPELVRL----TVGESAPA 252

Query: 509 SHSSP 513
           S   P
Sbjct: 253 SEYQP 257


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: 752
Number of extensions: 36
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 521
Length of database: 525
Length adjustment: 35
Effective length of query: 486
Effective length of database: 490
Effective search space:   238140
Effective search space used:   238140
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.

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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 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