Alignments for a candidate for HSERO_RS05250 in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Alignments for a candidate for HSERO_RS05250 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:D8J111
         (520 letters)



>FitnessBrowser__Phaeo:GFF2651
          Length = 522

 Score =  298 bits (763), Expect = 3e-85
 Identities = 173/496 (34%), Positives = 281/496 (56%), Gaps = 16/496 (3%)

Query: 21  PVIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDIL 80
           PV+ L+N+ KRF  V A D+  F+L  GEV AL+GENGAGK+TLM IL G Y  D+G + 
Sbjct: 14  PVLRLQNITKRFGSVTANDDVSFDLFPGEVIALLGENGAGKTTLMNILFGQYMADTGGVE 73

Query: 81  LDGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFIDEDELNRQ 140
           L G P+    PR A   G+G++HQ   L ++L+  +NI +G EP   +GL +       +
Sbjct: 74  LFGAPLPPGAPRAALDGGVGMVHQHFTLADNLTVWENITLGVEP--LLGLGLRAGPAKAR 131

Query: 141 AAAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAELF 200
             A+  +  L +DP+  V  LTV  +Q VEI KAL  D+R+LI+DEPTA L   E   LF
Sbjct: 132 IRALAEQFHLKVDPNAKVSRLTVGERQRVEILKALYRDARILILDEPTAVLTPQESDALF 191

Query: 201 RIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMVGRA 260
             +R+   +G+ +++ISHK+ E+  I+DRV V+R GK +A     +T  D + ++MVG  
Sbjct: 192 ATLREAINRGLSVIFISHKLHEVMAISDRVLVLRHGKLVAERQTADTDSDALAALMVGAD 251

Query: 261 LDGEQRIPPDTSRN---DVVLEVRGLNRGRA-----IRDVSFTLRKGEILGFAGLMGAGR 312
           +     +P   + N     +L++R +    A     +R VS  L  G+I G AG+ G G+
Sbjct: 252 V-----VPAKFAANTPGPALLQLRDVTTPSAGASPGLRHVSLDLAAGQITGLAGVSGNGQ 306

Query: 313 TEVARAIFGADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANI 372
             ++  + G    ++G + ++G      SP +A+  GI  + EDR   G     D+  N 
Sbjct: 307 AALSDLVSGLITPQSGSLTLNGAAPAGWSPREAITAGIARIPEDRHKTGTIADFDLTENA 366

Query: 373 ALSSMG-RFTRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLL 431
            L +   RF+  G++D RA R+ A+  +    ++ P  + + RLLSGGN QK+++ + L 
Sbjct: 367 ILETYATRFSHRGWLDWRAARDFAKTVITGYDVRCPGPDTRIRLLSGGNMQKLILGRVLE 426

Query: 432 RDCDILFFDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEG 491
           +   I+  ++P RG+D+GA + +++ L     +G A+++IS +L E++++S  + V+ EG
Sbjct: 427 QSPQIILANQPVRGLDIGAVTYVHEQLAKACARGAAVLLISEDLDEIMQLSDVIHVISEG 486

Query: 492 RITGELARADATQEKI 507
           R++   AR     E++
Sbjct: 487 RLSPGFARGSKQPEEL 502



 Score = 90.5 bits (223), Expect = 1e-22
 Identities = 67/225 (29%), Positives = 107/225 (47%), Gaps = 16/225 (7%)

Query: 291 DVSFTLRKGEILGFAGLMGAGRTEVARAIFGADPLEAGEIIIHGGKAVIKSPADAVAHGI 350
           DVSF L  GE++   G  GAG+T +   +FG    + G + + G      +P  A+  G+
Sbjct: 33  DVSFDLFPGEVIALLGENGAGKTTLMNILFGQYMADTGGVELFGAPLPPGAPRAALDGGV 92

Query: 351 GYLSEDRKHFGLAVGMDVQANIALSS---MGRFTRVGFMDQRAIREAAQMYVRQLAIKTP 407
           G + +   HF LA  + V  NI L     +G   R G    R    A Q +++       
Sbjct: 93  GMVHQ---HFTLADNLTVWENITLGVEPLLGLGLRAGPAKARIRALAEQFHLK------- 142

Query: 408 SVEQQARL--LSGGNQQKIVIAKWLLRDCDILFFDEPTRGIDVGAKSEIYKLLDALAEQG 465
            V+  A++  L+ G +Q++ I K L RD  IL  DEPT  +       ++  L     +G
Sbjct: 143 -VDPNAKVSRLTVGERQRVEILKALYRDARILILDEPTAVLTPQESDALFATLREAINRG 201

Query: 466 KAIVMISSELPEVLRMSHRVLVMCEGRITGELARADATQEKIMQL 510
            +++ IS +L EV+ +S RVLV+  G++  E   AD   + +  L
Sbjct: 202 LSVIFISHKLHEVMAISDRVLVLRHGKLVAERQTADTDSDALAAL 246



 Score = 65.5 bits (158), Expect = 5e-15
 Identities = 55/262 (20%), Positives = 115/262 (43%), Gaps = 14/262 (5%)

Query: 14  ASSSSSVPVIALRNVCKRFPGVL-ALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVY 72
           A+++    ++ LR+V     G    L +   +LAAG++  L G +G G++ L  ++SG+ 
Sbjct: 258 AANTPGPALLQLRDVTTPSAGASPGLRHVSLDLAAGQITGLAGVSGNGQAALSDLVSGLI 317

Query: 73  QRDSGDILLDGKPVEITEPRQAQALGIGIIHQELNLMNHLS---AAQNIFIGREPRKAMG 129
              SG + L+G       PR+A   GI  I ++ +    ++     +N  +     +   
Sbjct: 318 TPQSGSLTLNGAAPAGWSPREAITAGIARIPEDRHKTGTIADFDLTENAILETYATR--- 374

Query: 130 LFIDEDELNRQAAAIFARMRLD------MDPSTPVGELTVARQQMVEIAKALSFDSRVLI 183
            F     L+ +AA  FA+  +         P T +  L+    Q + + + L    ++++
Sbjct: 375 -FSHRGWLDWRAARDFAKTVITGYDVRCPGPDTRIRLLSGGNMQKLILGRVLEQSPQIIL 433

Query: 184 MDEPTAALNNAEIAELFRIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVP 243
            ++P   L+   +  +   +    A+G  ++ IS  +DE+ Q++D + V+ +G+      
Sbjct: 434 ANQPVRGLDIGAVTYVHEQLAKACARGAAVLLISEDLDEIMQLSDVIHVISEGRLSPGFA 493

Query: 244 MQETSMDTIISMMVGRALDGEQ 265
                 + + + M G   D  Q
Sbjct: 494 RGSKQPEELGAWMAGHGFDTPQ 515


Lambda     K      H
   0.320    0.135    0.372 

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: 598
Number of extensions: 33
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: 520
Length of database: 522
Length adjustment: 35
Effective length of query: 485
Effective length of database: 487
Effective search space:   236195
Effective search space used:   236195
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