Aligments for a candidate for ytfR in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Aligments 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)



>lcl|FitnessBrowser__Phaeo:GFF2651 PGA1_c26910 ABC transporter,
           ATP-binding protein
          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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Steps (tab-delimited)
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Protein sequences (fasta format)
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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 preprint 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