Alignments for a candidate for BPHYT_RS16930 in Trichormus variabilis ATCC 29413

GapMind for catabolism of small carbon sources

Alignments for a candidate for BPHYT_RS16930 in Trichormus variabilis ATCC 29413

Align Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale)
to candidate WP_011318959.1 AVA_RS10980 sugar ABC transporter ATP-binding protein

Query= uniprot:A0A165ZSX8
         (514 letters)



>NCBI__GCF_000204075.1:WP_011318959.1
          Length = 517

 Score =  388 bits (996), Expect = e-112
 Identities = 203/484 (41%), Positives = 314/484 (64%), Gaps = 7/484 (1%)

Query: 16  LRFNGIGKSFPGVQALANISFVAHPGQVHALMGENGAGKSTLLKILGGAYIPSSGDLQIG 75
           L   GI K F GV AL  ++   +PG+VHALMGENGAGKSTL+KIL GAYI   G+++I 
Sbjct: 19  LEMQGIAKRFHGVPALQGVNLTIYPGEVHALMGENGAGKSTLMKILAGAYIADEGEIRIN 78

Query: 76  EQTMAFKGTADSIASGVAVIHQELHLVPEMTVAENLFLGHLPARFGLVNRGVLRQQALTL 135
            + +       +  +G+ +I+QEL++ P +TV EN+F+G    R   ++R  +  +A  +
Sbjct: 79  GKGVKITDPGTARQAGINLIYQELNVAPNLTVTENIFMGSELTRGQFLDRKAMELEAQQV 138

Query: 136 LKGLADEIDPQEKVGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLMAIIG 195
           L  L     P + VG L++ ++Q VEIA+AL   + ++  DEPT++LS RE +RL  +I 
Sbjct: 139 LASLGASFAPTDIVGTLAIAEQQQVEIARALKDNSRILVMDEPTAALSDRETERLFEVIR 198

Query: 196 RLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTFENMSELTHDQLVTCMVGRDIQD 255
           +LR++G  ++Y+SHRMEE++ + + ++V +DG+Y+ +     E++  +LV  MVGR +QD
Sbjct: 199 KLRNDGIAIIYISHRMEEIYALADRISVLRDGQYIGSL-TREEISPQRLVQMMVGRSMQD 257

Query: 256 IYDY-RPRERGDVALQVKGLLGPGLHEPVSFQVHKGEILGLFGLVGAGRTELLRLLSGLE 314
            Y++ R    G V L+V+ +      +P SFQ+  GEILGL GLVGAGRTE+ RL+ G +
Sbjct: 258 FYEHQRQSNPGPVVLEVRNISDGRKVQPASFQLRAGEILGLAGLVGAGRTEVSRLIFGAD 317

Query: 315 RQREGSLVLHDKELKLRSPRDAIAAGVLLCPEDRKKEGIIPLGSVGENINISARPSHSTL 374
           R+  G + L+ K+L++ SP DAIA G+   PEDRK +G+    S  +NI ++     + L
Sbjct: 318 RKVSGEVFLNGKKLEIHSPSDAIAVGIGYVPEDRKDQGLFLEMSSRKNIGLNRLKQDANL 377

Query: 375 GCLLRGDWERGN--ADKQIKSLKVKTPTAGQKIMYLSGGNQQKAILGRWLSMPMKVLLLD 432
           G +   +W   N  A   +++  ++      + + LSGGNQQK +L RWL++  +VL+LD
Sbjct: 378 GIV---NWGSVNKIATDAVENFHIRLANLEIRAVDLSGGNQQKLLLARWLAINPRVLMLD 434

Query: 433 EPTRGIDIGAKAEIYQIIHNLAADGIAVIVVSSDLMEVMGISDRILVLCEGAMRGELSRD 492
           EPTRG+DIGAK+EIY+II +L+A G+A+++VSS+L E++G+SDR+LV+ EG + GEL   
Sbjct: 435 EPTRGVDIGAKSEIYRIISDLSAQGVAILMVSSELPEIVGLSDRVLVMREGQLVGELDNS 494

Query: 493 QANE 496
              E
Sbjct: 495 IGKE 498



 Score = 91.7 bits (226), Expect = 6e-23
 Identities = 70/254 (27%), Positives = 126/254 (49%), Gaps = 13/254 (5%)

Query: 258 DYRPRERGDVALQVKGLL----GPGLHEPVSFQVHKGEILGLFGLVGAGRTELLRLLSGL 313
           D+ P       L+++G+     G    + V+  ++ GE+  L G  GAG++ L+++L+G 
Sbjct: 8   DFSPPATATPVLEMQGIAKRFHGVPALQGVNLTIYPGEVHALMGENGAGKSTLMKILAGA 67

Query: 314 ERQREGSLVLHDKELKLRSPRDAIAAGVLLCPEDRKKEGIIPLGSVGENINISARPSHST 373
               EG + ++ K +K+  P  A  AG+ L  ++     + P  +V ENI +    S  T
Sbjct: 68  YIADEGEIRINGKGVKITDPGTARQAGINLIYQELN---VAPNLTVTENIFMG---SELT 121

Query: 374 LGCLLRGDWERGNADKQIKSLKVK-TPTAGQKIMYLSGGNQQKAILGRWLSMPMKVLLLD 432
            G  L        A + + SL     PT    +  L+   QQ+  + R L    ++L++D
Sbjct: 122 RGQFLDRKAMELEAQQVLASLGASFAPT--DIVGTLAIAEQQQVEIARALKDNSRILVMD 179

Query: 433 EPTRGIDIGAKAEIYQIIHNLAADGIAVIVVSSDLMEVMGISDRILVLCEGAMRGELSRD 492
           EPT  +       ++++I  L  DGIA+I +S  + E+  ++DRI VL +G   G L+R+
Sbjct: 180 EPTAALSDRETERLFEVIRKLRNDGIAIIYISHRMEEIYALADRISVLRDGQYIGSLTRE 239

Query: 493 QANESNLLQLALPR 506
           + +   L+Q+ + R
Sbjct: 240 EISPQRLVQMMVGR 253


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: 634
Number of extensions: 31
Number of successful extensions: 8
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: 517
Length adjustment: 35
Effective length of query: 479
Effective length of database: 482
Effective search space:   230878
Effective search space used:   230878
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 Apr 09 2024. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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 2024 update 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