GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ytfR in Herbaspirillum seropedicae SmR1

Align galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized)
to candidate HSERO_RS05250 HSERO_RS05250 D-ribose transporter ATP binding protein

Query= ecocyc::YTFR-MONOMER
         (500 letters)



>FitnessBrowser__HerbieS:HSERO_RS05250
          Length = 520

 Score =  361 bits (927), Expect = e-104
 Identities = 192/489 (39%), Positives = 299/489 (61%), Gaps = 4/489 (0%)

Query: 9   ILRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWL 68
           ++    + K FPGV ALDN  F L  GE+ AL+GENGAGKSTL+K L+GVY  D G I L
Sbjct: 22  VIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDILL 81

Query: 69  EGQAISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGREPKR-FGL-LRRKEMEKRA 126
           +G+ +       AQ LGIG ++QE+NL+ ++S A N+FIGREP++  GL +   E+ ++A
Sbjct: 82  DGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFIDEDELNRQA 141

Query: 127 TELMASYGFSLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFD 186
             + A     +D   P+   +VA QQ+V I +A+   ++VLI+DEPTA+L+  E+  LF 
Sbjct: 142 AAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAELFR 201

Query: 187 LMRQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMMLGREL 246
           ++R L+ +GV +++++H +D++ Q++DR++V+R+G ++      E     ++ MM+GR L
Sbjct: 202 IIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMVGRAL 261

Query: 247 DTHALQRAGRTLLSDKPVAAFKNYGKKGTIAPFDLEVRPGEIVGLAGLLGSGRTETAEVI 306
           D    QR       +  V   +   +   I      +R GEI+G AGL+G+GRTE A  I
Sbjct: 262 DGE--QRIPPDTSRNDVVLEVRGLNRGRAIRDVSFTLRKGEILGFAGLMGAGRTEVARAI 319

Query: 307 FGIKPADSGTALIKGKPQNLRSPHQASVLGIGFCPEDRKTDGIIAAASVRENIILALQAQ 366
           FG  P ++G  +I G    ++SP  A   GIG+  EDRK  G+     V+ NI L+   +
Sbjct: 320 FGADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSSMGR 379

Query: 367 RGWLRPISRKEQQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTRPQFLIL 426
              +  + ++  +E A+ ++RQL I+TPS EQ    LSGGNQQK+++++WLL     L  
Sbjct: 380 FTRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLRDCDILFF 439

Query: 427 DEPTRGIDVGAHAEIIRLIETLCADGLALLVISSELEELVGYADRVIIMRDRKQVAEIPL 486
           DEPTRGIDVGA +EI +L++ L   G A+++ISSEL E++  + RV++M + +   E+  
Sbjct: 440 DEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITGELAR 499

Query: 487 AELSVPAIM 495
           A+ +   IM
Sbjct: 500 ADATQEKIM 508



 Score =  111 bits (278), Expect = 5e-29
 Identities = 78/242 (32%), Positives = 127/242 (52%), Gaps = 10/242 (4%)

Query: 260 SDKPVAAFKNYGKK--GTIA--PFDLEVRPGEIVGLAGLLGSGRTETAEVIFGIKPADSG 315
           S  PV A +N  K+  G +A      E+  GE+  L G  G+G++   +++ G+   DSG
Sbjct: 18  SSVPVIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSG 77

Query: 316 TALIKGKPQNLRSPHQASVLGIGFCPEDRKTDGIIAAASVRENIILALQAQRGWLRPISR 375
             L+ GKP  +  P QA  LGIG   ++      ++AA   +NI +  + ++     I  
Sbjct: 78  DILLDGKPVEITEPRQAQALGIGIIHQELNLMNHLSAA---QNIFIGREPRKAMGLFIDE 134

Query: 376 KE-QQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTRPQFLILDEPTRGID 434
            E  ++ A  F R      PST  P+  L+   QQ V +++ L    + LI+DEPT  ++
Sbjct: 135 DELNRQAAAIFARMRLDMDPST--PVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALN 192

Query: 435 VGAHAEIIRLIETLCADGLALLVISSELEELVGYADRVIIMRDRKQVAEIPLAELSVPAI 494
               AE+ R+I  L A G+ ++ IS +++EL   ADRV +MRD K +A +P+ E S+  I
Sbjct: 193 NAEIAELFRIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTI 252

Query: 495 MN 496
           ++
Sbjct: 253 IS 254



 Score = 78.2 bits (191), Expect = 7e-19
 Identities = 58/249 (23%), Positives = 116/249 (46%), Gaps = 10/249 (4%)

Query: 3   TDQHQEILRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHAD 62
           T ++  +L   GL++     +A+ +V F+LR+GEI+   G  GAG++ + +A+ G    +
Sbjct: 271 TSRNDVVLEVRGLNRG----RAIRDVSFTLRKGEILGFAGLMGAGRTEVARAIFGADPLE 326

Query: 63  RGTIWLEGQAISPKNTAHAQQLGIGTVYQE---VNLLPNMSVADNLFIGREPK--RFGLL 117
            G I + G     K+ A A   GIG + ++     L   M V  N+ +    +  R G +
Sbjct: 327 AGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSSMGRFTRVGFM 386

Query: 118 RRKEMEKRATELMASYGFSL-DVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASL 176
            ++ + + A   +         V +     S   QQ + I + +     +L  DEPT  +
Sbjct: 387 DQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLRDCDILFFDEPTRGI 446

Query: 177 DTQEVELLFDLMRQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIE 236
           D      ++ L+  L ++G +++ ++  L +V ++S R+ V+  G   G     +  Q +
Sbjct: 447 DVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITGELARADATQEK 506

Query: 237 LVKMMLGRE 245
           ++++   RE
Sbjct: 507 IMQLATQRE 515


Lambda     K      H
   0.321    0.138    0.391 

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: 25
Number of successful extensions: 7
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: 500
Length of database: 520
Length adjustment: 34
Effective length of query: 466
Effective length of database: 486
Effective search space:   226476
Effective search space used:   226476
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:

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