Aligments for a candidate for ytfR in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Aligments 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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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, 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

GapMind for catabolism of small carbon sources