Alignments for a candidate for HSERO_RS03640 in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Alignments for a candidate for HSERO_RS03640 in Phaeobacter inhibens BS107

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate GFF2651 PGA1_c26910 ABC transporter, ATP-binding protein

Query= uniprot:D8IZC7
         (521 letters)



>FitnessBrowser__Phaeo:GFF2651
          Length = 522

 Score =  282 bits (721), Expect = 2e-80
 Identities = 172/494 (34%), Positives = 277/494 (56%), Gaps = 8/494 (1%)

Query: 4   TPLLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEI 63
           TP+L+++ I K FG+  A  D+   + PGE+ AL+GENGAGK+TLM +L G +  D G +
Sbjct: 13  TPVLRLQNITKRFGSVTANDDVSFDLFPGEVIALLGENGAGKTTLMNILFGQYMADTGGV 72

Query: 64  LLDGRPVALRDPGASRAA---GINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAM 120
            L G P+    PGA RAA   G+ +++Q   +A N++V  N+ +G E    LGL    A 
Sbjct: 73  ELFGAPLP---PGAPRAALDGGVGMVHQHFTLADNLTVWENITLGVEPLLGLGLRAGPA- 128

Query: 121 RSRTDAVLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETE 180
           ++R  A+  Q       +    RL++ E+Q+VEI +AL   +RI+I+DEPTA L+ +E++
Sbjct: 129 KARIRALAEQFHLKVDPNAKVSRLTVGERQRVEILKALYRDARILILDEPTAVLTPQESD 188

Query: 181 QLFNVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMV 240
            LF  +R   + GL++I+ISH++ EV A++DRV VLR G  V E    + DS+ +  +MV
Sbjct: 189 ALFATLREAINRGLSVIFISHKLHEVMAISDRVLVLRHGKLVAERQTADTDSDALAALMV 248

Query: 241 GRSLSEFYQHQRIAPADAAQLPTVMQVRALAGGKIRPASFDVRAGEVLGFAGLVGAGRTE 300
           G  +               QL  V    A A   +R  S D+ AG++ G AG+ G G+  
Sbjct: 249 GADVVPAKFAANTPGPALLQLRDVTTPSAGASPGLRHVSLDLAAGQITGLAGVSGNGQAA 308

Query: 301 LARLLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANATM 360
           L+ L+ G      G + L G       PR A+ AGIA +PEDR   G      +  NA +
Sbjct: 309 LSDLVSGLITPQSGSLTLNGAAPAGWSPREAITAGIARIPEDRHKTGTIADFDLTENAIL 368

Query: 361 NV-ASRHTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEIA 419
              A+R +  G +  R+    A+  I   +V+   P+T +  LSGGN QK++L R LE +
Sbjct: 369 ETYATRFSHRGWLDWRAARDFAKTVITGYDVRCPGPDTRIRLLSGGNMQKLILGRVLEQS 428

Query: 420 PKVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREGMI 479
           P++++ ++P RG+DI A + +++ + +  ++G AV++IS +L E++ + D + V+ EG +
Sbjct: 429 PQIILANQPVRGLDIGAVTYVHEQLAKACARGAAVLLISEDLDEIMQLSDVIHVISEGRL 488

Query: 480 TGELAGAAITQENI 493
           +   A  +   E +
Sbjct: 489 SPGFARGSKQPEEL 502



 Score = 97.8 bits (242), Expect = 8e-25
 Identities = 75/238 (31%), Positives = 118/238 (49%), Gaps = 11/238 (4%)

Query: 279 SFDVRAGEVLGFAGLVGAGRTELARLLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAY 338
           SFD+  GEV+   G  GAG+T L  +LFG      G + L G P+    PRAA+  G+  
Sbjct: 35  SFDLFPGEVIALLGENGAGKTTLMNILFGQYMADTGGVELFGAPLPPGAPRAALDGGVGM 94

Query: 339 VPEDRKGQGLFLQMAVAANATMNVASRHTRLGL-VRSRSLGGVARAAIQRLNVKVAHPET 397
           V +      L   + V  N T+ V      LGL +R+       RA  ++ ++KV  P  
Sbjct: 95  VHQHFT---LADNLTVWENITLGV---EPLLGLGLRAGPAKARIRALAEQFHLKV-DPNA 147

Query: 398 PVGKLSGGNQQKVLLARWLEIAPKVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVI 457
            V +L+ G +Q+V + + L    ++LILDEPT  +       ++  +    ++G++V+ I
Sbjct: 148 KVSRLTVGERQRVEILKALYRDARILILDEPTAVLTPQESDALFATLREAINRGLSVIFI 207

Query: 458 SSELPEVIGICDRVLVMREGMITGELAGAAITQENIMRLATDTNVPRTAPASHSSPTP 515
           S +L EV+ I DRVLV+R G +  E   A    + +  L    +V    PA  ++ TP
Sbjct: 208 SHKLHEVMAISDRVLVLRHGKLVAERQTADTDSDALAALMVGADV---VPAKFAANTP 262



 Score = 62.0 bits (149), Expect = 5e-14
 Identities = 57/243 (23%), Positives = 101/243 (41%), Gaps = 7/243 (2%)

Query: 6   LLQMRGIRK-SFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEIL 64
           LLQ+R +   S GA+  L  + L +  G+I  L G +G G++ L  ++SG+  P  G + 
Sbjct: 266 LLQLRDVTTPSAGASPGLRHVSLDLAAGQITGLAGVSGNGQAALSDLVSGLITPQSGSLT 325

Query: 65  LDGRPVALRDPGASRAAGINLIYQE---LAVAPNISVAANVFMGSELR--TRLGLIDHAA 119
           L+G   A   P  +  AGI  I ++        +  +  N  + +     +  G +D  A
Sbjct: 326 LNGAAPAGWSPREAITAGIARIPEDRHKTGTIADFDLTENAILETYATRFSHRGWLDWRA 385

Query: 120 MRSRTDAVLRQLGAGFGASDLAGRL-SIAEQQQVEIARALVHRSRIVIMDEPTAALSERE 178
            R     V+          D   RL S    Q++ + R L    +I++ ++P   L    
Sbjct: 386 ARDFAKTVITGYDVRCPGPDTRIRLLSGGNMQKLILGRVLEQSPQIILANQPVRGLDIGA 445

Query: 179 TEQLFNVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQM 238
              +   + +    G A++ IS  + E+  L+D + V+ +G       R     E +   
Sbjct: 446 VTYVHEQLAKACARGAAVLLISEDLDEIMQLSDVIHVISEGRLSPGFARGSKQPEELGAW 505

Query: 239 MVG 241
           M G
Sbjct: 506 MAG 508


Lambda     K      H
   0.320    0.135    0.378 

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: 667
Number of extensions: 36
Number of successful extensions: 8
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: 521
Length of database: 522
Length adjustment: 35
Effective length of query: 486
Effective length of database: 487
Effective search space:   236682
Effective search space used:   236682
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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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