Alignments for a candidate for ytfR in Herbaspirillum seropedicae SmR1

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_RS05175 HSERO_RS05175 sugar ABC transporter ATP-binding protein

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



>FitnessBrowser__HerbieS:HSERO_RS05175
          Length = 516

 Score =  467 bits (1202), Expect = e-136
 Identities = 250/505 (49%), Positives = 338/505 (66%), Gaps = 10/505 (1%)

Query: 5   QHQEILRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRG 64
           Q + +L   G+ K F GVKAL +V   L  GE+  L+G+NGAGKSTLIK LTGV+  D G
Sbjct: 8   QARPMLELSGIHKAFAGVKALTDVGLRLFPGEVHTLMGQNGAGKSTLIKVLTGVHEPDGG 67

Query: 65  TIWLEGQAISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGREPKRFGLLRRKEMEK 124
            I L+G+AI+P +T  AQ LGI TVYQEVNL PN+SVA+N+F+GR P RFG +  K +  
Sbjct: 68  KIELDGRAIAPASTLEAQALGISTVYQEVNLCPNLSVAENIFVGRYPTRFGRIDWKSVHT 127

Query: 125 RATELMASYGFSLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELL 184
           ++ +L+      +DV  PL+ + +A+QQ+VAI RA+ +SAKVLILDEPT+SLD  EV+ L
Sbjct: 128 QSRQLLQQLQIDIDVAAPLSSYPLAIQQMVAISRALSVSAKVLILDEPTSSLDEAEVQQL 187

Query: 185 FDLMRQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMMLGR 244
           F ++R+LR++G++++FVTHFLDQ Y++SDRITVLRNG   G     EL +++LV  M+G 
Sbjct: 188 FKVLRRLREQGMAILFVTHFLDQTYEISDRITVLRNGVREGEYLVSELSRLDLVNKMVGV 247

Query: 245 ELDTHALQRAGRTLLSDK-------PVAAF---KNYGKKGTIAPFDLEVRPGEIVGLAGL 294
               H    AG   L+ +         A F   + +G++G +AP DL++R GE+ GL GL
Sbjct: 248 TAVDHRKVEAGAEALASELSTDAAAAGAVFLQAEGFGRRGVLAPQDLQLRRGEVFGLCGL 307

Query: 295 LGSGRTETAEVIFGIKPADSGTALIKGKPQNLRSPHQASVLGIGFCPEDRKTDGIIAAAS 354
           LGSGRTE A ++FG   AD G   I+GK   L  P  A   GIGFC EDRK +G I   S
Sbjct: 308 LGSGRTEMARLLFGADRADCGQLRIEGKEVRLNVPRDAIAAGIGFCSEDRKKEGAILELS 367

Query: 355 VRENIILALQAQRGWLRPISRKEQQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLS 414
           VRENIILALQA++G  R + RK Q +IA  +++ LGI+T   E PI  LSGGNQQK LL+
Sbjct: 368 VRENIILALQARQGLFRVLPRKRQNQIAADYVKWLGIKTADLETPIGLLSGGNQQKALLA 427

Query: 415 RWLLTRPQFLILDEPTRGIDVGAHAEIIRLIETLCADGLALLVISSELEELVGYADRVII 474
           RWL T P  LILDEPTRGIDV A  EI+  +  +C  G+++L ISSE+ E++  +DR+++
Sbjct: 428 RWLATDPGMLILDEPTRGIDVRAKQEIMDFVIAMCRKGMSILFISSEIPEVLRCSDRMLV 487

Query: 475 MRDRKQVAEIPLAELSVPAIMNAIA 499
           +RDR+   E    EL   +++  IA
Sbjct: 488 LRDRRACGEYRRGELDEQSVLQVIA 512



 Score = 88.2 bits (217), Expect = 6e-22
 Identities = 59/221 (26%), Positives = 112/221 (50%), Gaps = 6/221 (2%)

Query: 29  DFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWLEGQAISPKNTAHAQQLGIGT 88
           D  LRRGE+  L G  G+G++ + + L G   AD G + +EG+ +       A   GIG 
Sbjct: 293 DLQLRRGEVFGLCGLLGSGRTEMARLLFGADRADCGQLRIEGKEVRLNVPRDAIAAGIGF 352

Query: 89  VYQE---VNLLPNMSVADNLFIGREPKR--FGLLRRKEMEKRATELMASYGF-SLDVREP 142
             ++      +  +SV +N+ +  + ++  F +L RK   + A + +   G  + D+  P
Sbjct: 353 CSEDRKKEGAILELSVRENIILALQARQGLFRVLPRKRQNQIAADYVKWLGIKTADLETP 412

Query: 143 LNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFDLMRQLRDRGVSLIFVT 202
           +   S   QQ   + R +     +LILDEPT  +D +  + + D +  +  +G+S++F++
Sbjct: 413 IGLLSGGNQQKALLARWLATDPGMLILDEPTRGIDVRAKQEIMDFVIAMCRKGMSILFIS 472

Query: 203 HFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMMLG 243
             + +V + SDR+ VLR+    G     EL +  +++++ G
Sbjct: 473 SEIPEVLRCSDRMLVLRDRRACGEYRRGELDEQSVLQVIAG 513


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: 641
Number of extensions: 22
Number of successful extensions: 6
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: 500
Length of database: 516
Length adjustment: 34
Effective length of query: 466
Effective length of database: 482
Effective search space:   224612
Effective search space used:   224612
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)
SQLite3 databases

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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
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