Alignments for a candidate for BPHYT_RS16930 in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Alignments for a candidate for BPHYT_RS16930 in Phaeobacter inhibens BS107

Align Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale)
to candidate GFF2770 PGA1_c28130 ABC transporter, ATP-binding protein

Query= uniprot:B2SYR5
         (512 letters)



>FitnessBrowser__Phaeo:GFF2770
          Length = 505

 Score =  259 bits (663), Expect = 1e-73
 Identities = 168/484 (34%), Positives = 262/484 (54%), Gaps = 24/484 (4%)

Query: 5   LRFDNIGKVFPGVRALDGVSFDVNVGQVHGLMGENGAGKSTLLKILGGEYQPDSGRVMID 64
           L    + K +PGV A D VSFD+  G+VH L+GENGAGKSTL+K++ G  +PDSG++++ 
Sbjct: 6   LSLQGLTKAYPGVVANDTVSFDIGAGEVHALLGENGAGKSTLVKMIYGLVKPDSGKMLLH 65

Query: 65  GNEVRFTSAASSIAAGIAVIHQELQYVPDLTVAENLLLG-QLPNSLGWVNKREAKRFVRE 123
           G          + A GIA++ Q       L VAEN+ LG + P +L     R+    +R+
Sbjct: 66  GEPYTPGEPRQARADGIAMVFQHFSLFDALNVAENIALGMETPPAL-----RDLATQIRK 120

Query: 124 RLEAMGVALDPNAKLRKLSIAQRQMVEICKALLRNARVIALDEPTSSLSHRETEVLFKLV 183
             E  G+ LDP   +  LS  +RQ VEI + LL++ +++ +DEPTS L+ +E E+LF+ +
Sbjct: 121 VSETYGLPLDPYRTVGDLSAGERQRVEIIRCLLQDPKLLIMDEPTSVLTPQEVEILFQTL 180

Query: 184 RDLRADNRAMIYISHRMDEIYELCDACTIFRDGRKIASHPTLEGVTRDTIVSEMVGREIS 243
           + LR++  +++YISH+++EI  LCD  TI R G+ +      E   RD  ++EM+     
Sbjct: 181 QKLRSEGTSILYISHKLEEIRTLCDHATILRLGKNVGECVPSETSARD--MAEMMVGTAL 238

Query: 244 DIYNYSARPLGEVRFAAKGIEGHALAQPASF---------EVRRGEIVGFFGLVGAGRSE 294
                S R LG+V   A  I G ++  P++F          VR+GEI+G  G+ G G+ E
Sbjct: 239 QTPERSGRALGDV---ALDISGLSVPAPSAFGTALKNVHMTVRKGEILGVGGVAGNGQDE 295

Query: 295 LMHLVYGADHKKGGELLLDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINI 354
           L+ ++ G        + LDG PI         R GI+  PE+R         +++EN  +
Sbjct: 296 LLGVLSGETTTAADAVTLDGAPIGNLGPVARRRLGILAAPEERLGHAAAPDMSLTENAML 355

Query: 355 -SCRRHYLRVGMFLDRKKEAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSR-WLA 412
            +  R  L    FL      E A++ IK   ++TP      R LSGGN QK ++ R  L 
Sbjct: 356 TAATREGLASRGFLKWGLAQEFAEKVIKSFDVRTPGPENAARSLSGGNLQKFVIGREVLQ 415

Query: 413 EPDLKVVILDEPTRGIDVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQ 472
            PD  V+++++PT G+D  A   I   +  LA  G A++ IS +L E++ ++D    + +
Sbjct: 416 RPD--VLVVNQPTWGVDAAAAAAIRQSLLDLAAGGTAVICISQDLDELMEIADSFAALNE 473

Query: 473 GRIS 476
           GR+S
Sbjct: 474 GRLS 477



 Score = 71.2 bits (173), Expect = 8e-17
 Identities = 64/251 (25%), Positives = 111/251 (44%), Gaps = 15/251 (5%)

Query: 251 RPLGEVRFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELMHLVYGADHKKGGEL 310
           +PL  ++   K   G       SF++  GE+    G  GAG+S L+ ++YG      G++
Sbjct: 3   QPLLSLQGLTKAYPGVVANDTVSFDIGAGEVHALLGENGAGKSTLVKMIYGLVKPDSGKM 62

Query: 311 LLDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCRRHYLRVGMFLDRK 370
           LL G+P       +A   GI +     +   +     V+ENI +          +    +
Sbjct: 63  LLHGEPYTPGEPRQARADGIAMV---FQHFSLFDALNVAENIALGMETPPALRDLATQIR 119

Query: 371 KEAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWLAEPDLKVVILDEPTRGIDV 430
           K +ET    + L   +T      +  LS G +Q+  + R L + D K++I+DEPT  +  
Sbjct: 120 KVSETYG--LPLDPYRT------VGDLSAGERQRVEIIRCLLQ-DPKLLIMDEPTSVLTP 170

Query: 431 GAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRISGELTRKDATEQSVL 490
                ++  + +L   G +I+ IS +L E+  + D   ++R G+  GE      +E S  
Sbjct: 171 QEVEILFQTLQKLRSEGTSILYISHKLEEIRTLCDHATILRLGKNVGECV---PSETSAR 227

Query: 491 SLALPQSSTAL 501
            +A     TAL
Sbjct: 228 DMAEMMVGTAL 238



 Score = 70.1 bits (170), Expect = 2e-16
 Identities = 61/229 (26%), Positives = 101/229 (44%), Gaps = 9/229 (3%)

Query: 19  ALDGVSFDVNVGQVHGLMGENGAGKSTLLKILGGEYQPDSGRVMIDGNEVRFTSAASSIA 78
           AL  V   V  G++ G+ G  G G+  LL +L GE    +  V +DG  +      +   
Sbjct: 269 ALKNVHMTVRKGEILGVGGVAGNGQDELLGVLSGETTTAADAVTLDGAPIGNLGPVARRR 328

Query: 79  AGIAVIHQEL---QYVPDLTVAENLLLGQLPN----SLGWVNKREAKRFVRERLEAMGVA 131
            GI    +E       PD+++ EN +L         S G++    A+ F  + +++  V 
Sbjct: 329 LGILAAPEERLGHAAAPDMSLTENAMLTAATREGLASRGFLKWGLAQEFAEKVIKSFDVR 388

Query: 132 LD-PNAKLRKLSIAQRQMVEICKALLRNARVIALDEPTSSLSHRETEVLFKLVRDLRADN 190
              P    R LS    Q   I + +L+   V+ +++PT  +       + + + DL A  
Sbjct: 389 TPGPENAARSLSGGNLQKFVIGREVLQRPDVLVVNQPTWGVDAAAAAAIRQSLLDLAAGG 448

Query: 191 RAMIYISHRMDEIYELCDACTIFRDGRKIASHPTLEGVTRDTIVSEMVG 239
            A+I IS  +DE+ E+ D+     +GR  A  PT  G++ D I   M G
Sbjct: 449 TAVICISQDLDELMEIADSFAALNEGRLSAPRPT-AGLSVDEIGLMMGG 496


Lambda     K      H
   0.320    0.136    0.385 

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: 606
Number of extensions: 37
Number of successful extensions: 9
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: 512
Length of database: 505
Length adjustment: 34
Effective length of query: 478
Effective length of database: 471
Effective search space:   225138
Effective search space used:   225138
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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Protein sequences (fasta format)
Organisms (tab-delimited)
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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