GapMind for catabolism of small carbon sources

 

Aligments for a candidate for BPHYT_RS16930 in Herbaspirillum seropedicae SmR1

Align Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale)
to candidate HSERO_RS05250 HSERO_RS05250 D-ribose transporter ATP binding protein

Query= uniprot:B2SYR5
         (512 letters)



>lcl|FitnessBrowser__HerbieS:HSERO_RS05250 HSERO_RS05250 D-ribose
           transporter ATP binding protein
          Length = 520

 Score =  404 bits (1037), Expect = e-117
 Identities = 218/498 (43%), Positives = 324/498 (65%), Gaps = 16/498 (3%)

Query: 9   NIGKVFPGVRALDGVSFDVNVGQVHGLMGENGAGKSTLLKILGGEYQPDSGRVMIDGNEV 68
           N+ K FPGV ALD   F++  G+VH LMGENGAGKSTL+KIL G YQ DSG +++DG  V
Sbjct: 27  NVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDILLDGKPV 86

Query: 69  RFTSAASSIAAGIAVIHQELQYVPDLTVAENLLLGQLP-NSLGW------VNKREAKRFV 121
             T    + A GI +IHQEL  +  L+ A+N+ +G+ P  ++G       +N++ A  F 
Sbjct: 87  EITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFIDEDELNRQAAAIFA 146

Query: 122 RERLEAMGVALDPNAKLRKLSIAQRQMVEICKALLRNARVIALDEPTSSLSHRETEVLFK 181
           R RL+     +DP+  + +L++A++QMVEI KAL  ++RV+ +DEPT++L++ E   LF+
Sbjct: 147 RMRLD-----MDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAELFR 201

Query: 182 LVRDLRADNRAMIYISHRMDEIYELCDACTIFRDGRKIASHPTLEGVTRDTIVSEMVGRE 241
           ++RDL+A    ++YISH+MDE+ ++ D  ++ RDG+ IA+ P ++  + DTI+S MVGR 
Sbjct: 202 IIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVP-MQETSMDTIISMMVGRA 260

Query: 242 ISDIYNYSA-RPLGEVRFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELMHLVY 300
           +             +V    +G+      +  SF +R+GEI+GF GL+GAGR+E+   ++
Sbjct: 261 LDGEQRIPPDTSRNDVVLEVRGLNRGRAIRDVSFTLRKGEILGFAGLMGAGRTEVARAIF 320

Query: 301 GADHKKGGELLLDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCRRHY 360
           GAD  + GE+++ G    ++S  +A+ HGI    EDRK  G+     V  NI +S    +
Sbjct: 321 GADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSSMGRF 380

Query: 361 LRVGMFLDRKKEAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWLAEPDLKVVI 420
            RVG F+D++   E A  +++ L IKTPS  Q+ R LSGGNQQK ++++WL   D  ++ 
Sbjct: 381 TRVG-FMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLR-DCDILF 438

Query: 421 LDEPTRGIDVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRISGELT 480
            DEPTRGIDVGAK EIY ++  LAE+G AIVMISSELPEVL +S R++VM +GRI+GEL 
Sbjct: 439 FDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITGELA 498

Query: 481 RKDATEQSVLSLALPQSS 498
           R DAT++ ++ LA  + S
Sbjct: 499 RADATQEKIMQLATQRES 516



 Score = 93.6 bits (231), Expect = 2e-23
 Identities = 70/258 (27%), Positives = 130/258 (50%), Gaps = 11/258 (4%)

Query: 249 SARPLGEVRFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELMHLVYGADHKKGG 308
           S+ P+  +R   K   G        FE+  GE+    G  GAG+S LM ++ G   +  G
Sbjct: 18  SSVPVIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSG 77

Query: 309 ELLLDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCRRHYLRVGMFLD 368
           ++LLDGKP+++    +A   GI +     +E  ++   + ++NI I  R     +G+F+D
Sbjct: 78  DILLDGKPVEITEPRQAQALGIGII---HQELNLMNHLSAAQNIFIG-REPRKAMGLFID 133

Query: 369 RKK-EAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWLAEPDLKVVILDEPTRG 427
             +   + A  F ++     PS    +  L+   QQ   +++ L+  D +V+I+DEPT  
Sbjct: 134 EDELNRQAAAIFARMRLDMDPS--TPVGELTVARQQMVEIAKALSF-DSRVLIMDEPTAA 190

Query: 428 IDVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRISGELTRKDATEQ 487
           ++     E++ +I  L  +G  IV IS ++ E+  ++DR+ VMR G+    +  ++ +  
Sbjct: 191 LNNAEIAELFRIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMD 250

Query: 488 SVLSLALPQSSTALPGTQ 505
           +++S+ +     AL G Q
Sbjct: 251 TIISMMV---GRALDGEQ 265


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: 654
Number of extensions: 27
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: 520
Length adjustment: 35
Effective length of query: 477
Effective length of database: 485
Effective search space:   231345
Effective search space used:   231345
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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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:

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:

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:

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, or view the source code.

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