Alignments for a candidate for PS417_11890 in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Alignments for a candidate for PS417_11890 in Phaeobacter inhibens BS107

Align Inositol transport system ATP-binding protein (characterized)
to candidate GFF2651 PGA1_c26910 ABC transporter, ATP-binding protein

Query= reanno::WCS417:GFF2332
         (517 letters)



>FitnessBrowser__Phaeo:GFF2651
          Length = 522

 Score =  292 bits (747), Expect = 2e-83
 Identities = 175/511 (34%), Positives = 280/511 (54%), Gaps = 15/511 (2%)

Query: 2   LAQATVSQPPSLQPQTLEEPYLLEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAG 61
           +A   + Q P L P       +L + NI+K F  V A  DV   + PG V+AL+GENGAG
Sbjct: 1   MASDKMGQAPGLTP-------VLRLQNITKRFGSVTANDDVSFDLFPGEVIALLGENGAG 53

Query: 62  KSTLMKIIAGIYQPDAGEIRLRGKPIVFETPLAAQKAGIAMIHQELNLMPHMSIAENIWI 121
           K+TLM I+ G Y  D G + L G P+    P AA   G+ M+HQ   L  ++++ ENI +
Sbjct: 54  KTTLMNILFGQYMADTGGVELFGAPLPPGAPRAALDGGVGMVHQHFTLADNLTVWENITL 113

Query: 122 GREQLNSLHMVNHREMHRCTAELLARLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDI 181
           G E L  L +       R  A L  +  + +DP  +V  L++ ERQ VEI KA+  D+ I
Sbjct: 114 GVEPLLGLGLRAGPAKARIRA-LAEQFHLKVDPNAKVSRLTVGERQRVEILKALYRDARI 172

Query: 182 LIMDEPTSAITEKEVAHLFSIIADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIGL 241
           LI+DEPT+ +T +E   LF+ + +  ++G  +++I+HK++EV AI+D V V R G  +  
Sbjct: 173 LILDEPTAVLTPQESDALFATLREAINRGLSVIFISHKLHEVMAISDRVLVLRHGKLVAE 232

Query: 242 QRADSMNSDSLISMMVGRELSQLFPLRETPIGDLLLTVRDLTLDGV-----FKDVSFDLH 296
           ++    +SD+L ++MVG ++        TP G  LL +RD+T          + VS DL 
Sbjct: 233 RQTADTDSDALAALMVGADVVPAKFAANTP-GPALLQLRDVTTPSAGASPGLRHVSLDLA 291

Query: 297 AGEILGIAGLMGSGRTNVAETIFGITPSSSGQITLDGKAVRISDPHMAIEKGFALLTEDR 356
           AG+I G+AG+ G+G+  +++ + G+    SG +TL+G A     P  AI  G A + EDR
Sbjct: 292 AGQITGLAGVSGNGQAALSDLVSGLITPQSGSLTLNGAAPAGWSPREAITAGIARIPEDR 351

Query: 357 KLSGLFPCLSVLENMEM-AVLPHYTGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTL 415
             +G      + EN  +      ++  G++  +A R   + +     V+ P  +  I  L
Sbjct: 352 HKTGTIADFDLTENAILETYATRFSHRGWLDWRAARDFAKTVITGYDVRCPGPDTRIRLL 411

Query: 416 SGGNQQKALLARWLMTNPRLLILDEPTRGIDVGAKAEIYRLIAFLASEGMAVIMISSELP 475
           SGGN QK +L R L  +P++++ ++P RG+D+GA   ++  +A   + G AV++IS +L 
Sbjct: 412 SGGNMQKLILGRVLEQSPQIILANQPVRGLDIGAVTYVHEQLAKACARGAAVLLISEDLD 471

Query: 476 EVLGMSDRVMVMHEGELMGTLDRSEATQEKV 506
           E++ +SD + V+ EG L     R     E++
Sbjct: 472 EIMQLSDVIHVISEGRLSPGFARGSKQPEEL 502



 Score = 89.7 bits (221), Expect = 2e-22
 Identities = 66/230 (28%), Positives = 116/230 (50%), Gaps = 12/230 (5%)

Query: 290 DVSFDLHAGEILGIAGLMGSGRTNVAETIFGITPSSSGQITLDGKAVRISDPHMAIEKGF 349
           DVSFDL  GE++ + G  G+G+T +   +FG   + +G + L G  +    P  A++ G 
Sbjct: 33  DVSFDLFPGEVIALLGENGAGKTTLMNILFGQYMADTGGVELFGAPLPPGAPRAALDGGV 92

Query: 350 ALLTEDRKLSGLFPCLSVLENMEMAVLPHYTGNGFIQQKA---LRALCEDMCKKLRVKTP 406
            ++ +   L+     L+V EN+ + V P   G G     A   +RAL E    K+    P
Sbjct: 93  GMVHQHFTLADN---LTVWENITLGVEP-LLGLGLRAGPAKARIRALAEQFHLKV---DP 145

Query: 407 SLEQCIDTLSGGNQQKALLARWLMTNPRLLILDEPTRGIDVGAKAEIYRLIAFLASEGMA 466
           + +  +  L+ G +Q+  + + L  + R+LILDEPT  +       ++  +    + G++
Sbjct: 146 NAK--VSRLTVGERQRVEILKALYRDARILILDEPTAVLTPQESDALFATLREAINRGLS 203

Query: 467 VIMISSELPEVLGMSDRVMVMHEGELMGTLDRSEATQEKVMQLASGMTAV 516
           VI IS +L EV+ +SDRV+V+  G+L+     ++   + +  L  G   V
Sbjct: 204 VIFISHKLHEVMAISDRVLVLRHGKLVAERQTADTDSDALAALMVGADVV 253


Lambda     K      H
   0.320    0.136    0.381 

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: 601
Number of extensions: 33
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: 517
Length of database: 522
Length adjustment: 35
Effective length of query: 482
Effective length of database: 487
Effective search space:   234734
Effective search space used:   234734
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