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 GFF385 PGA1_c03960 ribose import ATP-binding protein RbsA

Query= uniprot:A0A165ZSX8
         (514 letters)



>FitnessBrowser__Phaeo:GFF385
          Length = 509

 Score =  255 bits (652), Expect = 2e-72
 Identities = 167/500 (33%), Positives = 265/500 (53%), Gaps = 22/500 (4%)

Query: 15  SLRFNGIGKSFPGVQALANISFVAHPGQVHALMGENGAGKSTLLKILGGAYIPSSGDLQI 74
           ++   GI K+F  VQA  +IS    PG +H ++GENGAGKSTL+ IL G Y    G++ I
Sbjct: 5   AIELKGISKAFGPVQANKDISIRVAPGTIHGIIGENGAGKSTLMSILYGFYKADKGEVWI 64

Query: 75  GEQTMAFKGTADSIASGVAVIHQELHLVPEMTVAENLFLGHLPARFGLVNRGVLRQQALT 134
             +      +  +I++G+ ++ Q   LV   TV EN+ LG      GL+   +   +A  
Sbjct: 65  HGKRTEIPDSQAAISAGIGMVFQHFKLVENFTVLENIILGAEDG--GLLKPSL--SKARK 120

Query: 135 LLKGLADE----IDPQEKVGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRL 190
            LK LA E    +DP  ++  + +G +Q VEI KAL R A ++  DEPT  L+  E D+L
Sbjct: 121 SLKDLAAEYELNVDPDARIDEIGVGMQQRVEILKALYRQADILILDEPTGVLTPAEADQL 180

Query: 191 MAIIGRLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTFENMSELTHDQLVTCMVG 250
             I+ RLR EGK ++ ++H++ E+    + V+V + G    T +  +E + + L   MVG
Sbjct: 181 FRILDRLRAEGKTIILITHKLREIMEYTDTVSVMRRGEMTATVKT-AETSPEHLAELMVG 239

Query: 251 RDIQDIYDYRPRERGDVALQVKGL-----LGPGLHEPVSFQVHKGEILGLFGLVGAGRTE 305
           R +    D  P   G   L+++ L      G    + +   V  GEILG+ G+ G G++E
Sbjct: 240 RKVLLRVDKVPATPGKPILEIENLSVVDEAGVARVKNIDLTVRAGEILGIAGVAGNGQSE 299

Query: 306 LLRLLSGLERQREGSLVLHDKELKLRSP----RDAIAAGVLLCPEDRKKEGIIPLGSVGE 361
           L+ +L G+ R+ +GS+ L+   L L       R   AA V   PEDR++EG+I      E
Sbjct: 300 LMEVLGGM-REGQGSIRLNGAPLPLSGAGSDARARRAAHVAHVPEDRQREGLIMDFHAWE 358

Query: 362 NINISAR--PSHSTLGCLLRGDWERGNADKQIKSLKVKTPTAGQKIMYLSGGNQQKAILG 419
           N+       P +   G L+     R + + ++    V+ P         SGGNQQK ++ 
Sbjct: 359 NVAFGYHHAPEYQR-GLLMNNAALRADTEAKMAKFDVRPPDPWLAAKNFSGGNQQKIVVA 417

Query: 420 RWLSMPMKVLLLDEPTRGIDIGAKAEIYQIIHNLAADGIAVIVVSSDLMEVMGISDRILV 479
           R +    ++LL+ +PTRG+DIGA   I++ I  L   G A+++VS +L E++ ++DR+ V
Sbjct: 418 REIERNPELLLIGQPTRGVDIGAIEFIHKQIVELRDQGKAILLVSVELEEILSLADRVAV 477

Query: 480 LCEGAMRGELSRDQANESNL 499
           + +G + GE   DQ +E  L
Sbjct: 478 MFDGMIMGERPADQTDEKEL 497



 Score = 77.8 bits (190), Expect = 9e-19
 Identities = 65/249 (26%), Positives = 126/249 (50%), Gaps = 21/249 (8%)

Query: 268 ALQVKGL---LGP-GLHEPVSFQVHKGEILGLFGLVGAGRTELLRLLSGLERQREGSLVL 323
           A+++KG+    GP   ++ +S +V  G I G+ G  GAG++ L+ +L G  +  +G + +
Sbjct: 5   AIELKGISKAFGPVQANKDISIRVAPGTIHGIIGENGAGKSTLMSILYGFYKADKGEVWI 64

Query: 324 HDKELKLRSPRDAIAAGVLLCPEDRKKEGIIPLGSVGENINISARPSHSTLGCLLRGDWE 383
           H K  ++   + AI+AG+ +  +  K   ++   +V ENI + A       G LL+    
Sbjct: 65  HGKRTEIPDSQAAISAGIGMVFQHFK---LVENFTVLENIILGAED-----GGLLKPSLS 116

Query: 384 RGNADKQIKSLKVK-----TPTAGQKIMYLSGGNQQKAILGRWLSMPMKVLLLDEPTRGI 438
           +  A K +K L  +      P A  +I  +  G QQ+  + + L     +L+LDEPT  +
Sbjct: 117 K--ARKSLKDLAAEYELNVDPDA--RIDEIGVGMQQRVEILKALYRQADILILDEPTGVL 172

Query: 439 DIGAKAEIYQIIHNLAADGIAVIVVSSDLMEVMGISDRILVLCEGAMRGELSRDQANESN 498
                 ++++I+  L A+G  +I+++  L E+M  +D + V+  G M   +   + +  +
Sbjct: 173 TPAEADQLFRILDRLRAEGKTIILITHKLREIMEYTDTVSVMRRGEMTATVKTAETSPEH 232

Query: 499 LLQLALPRQ 507
           L +L + R+
Sbjct: 233 LAELMVGRK 241


Lambda     K      H
   0.320    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: 680
Number of extensions: 33
Number of successful extensions: 9
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: 514
Length of database: 509
Length adjustment: 35
Effective length of query: 479
Effective length of database: 474
Effective search space:   227046
Effective search space used:   227046
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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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