GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ytfR in Phaeobacter inhibens BS107

Align galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized)
to candidate GFF2651 PGA1_c26910 ABC transporter, ATP-binding protein

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



>FitnessBrowser__Phaeo:GFF2651
          Length = 522

 Score =  266 bits (679), Expect = 2e-75
 Identities = 165/475 (34%), Positives = 257/475 (54%), Gaps = 10/475 (2%)

Query: 9   ILRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWL 68
           +LR + ++K F  V A D+V F L  GE++ALLGENGAGK+TL+  L G Y AD G + L
Sbjct: 15  VLRLQNITKRFGSVTANDDVSFDLFPGEVIALLGENGAGKTTLMNILFGQYMADTGGVEL 74

Query: 69  EGQAISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGREPKRFGLLRRKEMEKRATE 128
            G  + P     A   G+G V+Q   L  N++V +N+ +G EP     LR    + R   
Sbjct: 75  FGAPLPPGAPRAALDGGVGMVHQHFTLADNLTVWENITLGVEPLLGLGLRAGPAKARIRA 134

Query: 129 LMASYGFSLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFDLM 188
           L   +   +D    ++R +V  +Q V I +A+   A++LILDEPTA L  QE + LF  +
Sbjct: 135 LAEQFHLKVDPNAKVSRLTVGERQRVEILKALYRDARILILDEPTAVLTPQESDALFATL 194

Query: 189 RQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMMLGREL-- 246
           R+  +RG+S+IF++H L +V  +SDR+ VLR+G  V  R+T +     L  +M+G ++  
Sbjct: 195 REAINRGLSVIFISHKLHEVMAISDRVLVLRHGKLVAERQTADTDSDALAALMVGADVVP 254

Query: 247 DTHALQRAGRTLLSDKPVAAFKNYGKKGTIAPFDLEVRPGEIVGLAGLLGSGRTETAEVI 306
              A    G  LL  + V    + G    +    L++  G+I GLAG+ G+G+   ++++
Sbjct: 255 AKFAANTPGPALLQLRDVTT-PSAGASPGLRHVSLDLAAGQITGLAGVSGNGQAALSDLV 313

Query: 307 FGIKPADSGTALIKGKPQNLRSPHQASVLGIGFCPEDRKTDGIIAAASVRENIILALQA- 365
            G+    SG+  + G      SP +A   GI   PEDR   G IA   + EN IL   A 
Sbjct: 314 SGLITPQSGSLTLNGAAPAGWSPREAITAGIARIPEDRHKTGTIADFDLTENAILETYAT 373

Query: 366 ---QRGWLRPISRKEQQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTRPQ 422
               RGWL     +  ++ A+  I    +R P  +  I  LSGGN QK++L R L   PQ
Sbjct: 374 RFSHRGWL---DWRAARDFAKTVITGYDVRCPGPDTRIRLLSGGNMQKLILGRVLEQSPQ 430

Query: 423 FLILDEPTRGIDVGAHAEIIRLIETLCADGLALLVISSELEELVGYADRVIIMRD 477
            ++ ++P RG+D+GA   +   +   CA G A+L+IS +L+E++  +D + ++ +
Sbjct: 431 IILANQPVRGLDIGAVTYVHEQLAKACARGAAVLLISEDLDEIMQLSDVIHVISE 485



 Score = 72.8 bits (177), Expect = 3e-17
 Identities = 66/238 (27%), Positives = 117/238 (49%), Gaps = 14/238 (5%)

Query: 263 PVAAFKNYGKK-GTIAPFD---LEVRPGEIVGLAGLLGSGRTETAEVIFGIKPADSGTAL 318
           PV   +N  K+ G++   D    ++ PGE++ L G  G+G+T    ++FG   AD+G   
Sbjct: 14  PVLRLQNITKRFGSVTANDDVSFDLFPGEVIALLGENGAGKTTLMNILFGQYMADTGGVE 73

Query: 319 IKGKPQNLRSPHQASVLGIGFCPEDRKTDGIIAAASVRENIILALQAQRGW-LRPISRKE 377
           + G P    +P  A   G+G   +      +    +V ENI L ++   G  LR    K 
Sbjct: 74  LFGAPLPPGAPRAALDGGVGMVHQHFT---LADNLTVWENITLGVEPLLGLGLRAGPAKA 130

Query: 378 Q-QEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTRPQFLILDEPTRGIDVG 436
           + + +AE+F  ++    P+ +  +  L+ G +Q+V + + L    + LILDEPT  +   
Sbjct: 131 RIRALAEQFHLKVD---PNAK--VSRLTVGERQRVEILKALYRDARILILDEPTAVLTPQ 185

Query: 437 AHAEIIRLIETLCADGLALLVISSELEELVGYADRVIIMRDRKQVAEIPLAELSVPAI 494
               +   +      GL+++ IS +L E++  +DRV+++R  K VAE   A+    A+
Sbjct: 186 ESDALFATLREAINRGLSVIFISHKLHEVMAISDRVLVLRHGKLVAERQTADTDSDAL 243



 Score = 59.3 bits (142), Expect = 3e-13
 Identities = 55/236 (23%), Positives = 104/236 (44%), Gaps = 17/236 (7%)

Query: 25  LDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWLEGQAISPKNTAHAQQL 84
           L +V   L  G+I  L G +G G++ L   ++G+     G++ L G A +  +   A   
Sbjct: 283 LRHVSLDLAAGQITGLAGVSGNGQAALSDLVSGLITPQSGSLTLNGAAPAGWSPREAITA 342

Query: 85  GIGTVYQE---VNLLPNMSVADNLFIGREPKRF---GLLRRKEMEKRATELMASYGFSLD 138
           GI  + ++      + +  + +N  +     RF   G L  +     A  ++  Y    D
Sbjct: 343 GIARIPEDRHKTGTIADFDLTENAILETYATRFSHRGWLDWRAARDFAKTVITGY----D 398

Query: 139 VREP-----LNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFDLMRQLRD 193
           VR P     +   S    Q + + R ++ S ++++ ++P   LD   V  + + + +   
Sbjct: 399 VRCPGPDTRIRLLSGGNMQKLILGRVLEQSPQIILANQPVRGLDIGAVTYVHEQLAKACA 458

Query: 194 RGVSLIFVTHFLDQVYQVSDRITVLRNGSF-VGCRETCELPQIELVKMMLGRELDT 248
           RG +++ ++  LD++ Q+SD I V+  G    G     + P+ EL   M G   DT
Sbjct: 459 RGAAVLLISEDLDEIMQLSDVIHVISEGRLSPGFARGSKQPE-ELGAWMAGHGFDT 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: 554
Number of extensions: 29
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: 522
Length adjustment: 35
Effective length of query: 465
Effective length of database: 487
Effective search space:   226455
Effective search space used:   226455
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