Alignments for a candidate for BPHYT_RS34245 in Halomonas desiderata SP1

GapMind for catabolism of small carbon sources

Alignments for a candidate for BPHYT_RS34245 in Halomonas desiderata SP1

Align ABC transporter related; Flags: Precursor (characterized, see rationale)
to candidate WP_086510989.1 BZY95_RS16555 L-arabinose ABC transporter ATP-binding protein AraG

Query= uniprot:B2T9V9
         (510 letters)



>NCBI__GCF_002151265.1:WP_086510989.1
          Length = 497

 Score =  260 bits (665), Expect = 7e-74
 Identities = 161/473 (34%), Positives = 257/473 (54%), Gaps = 12/473 (2%)

Query: 24  FGSTAALNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPDTGEVRFSGAAAPSIAD 83
           F    AL+ VS     G+ HAL+G NGAGKSTL+ +L+G+  P  G +   G        
Sbjct: 15  FPGVRALDGVSFGAHAGQVHALMGENGAGKSTLLKVLSGVNHPSEGALWIDGERHVFANA 74

Query: 84  RDAWRERVACVYQHSTIIRDLSVAENLFINRQPLRGGVIDWQAMRRDARALL-DHWKIDV 142
           R+A  + +A +YQ  T+  +++VAENL + + P R G I  + +R  A A+L D  + D+
Sbjct: 75  REALAQGIAIIYQELTLSPNMTVAENLLLGQLPTRHGFIKRRQLRERALAILADLGEGDI 134

Query: 143 REDARAGDLSVEARQLVEIARALSYGARFIILDEPTAQLDGDEIKRLFRRISELQREGVT 202
               +  +LS+  +Q++EI RAL   AR I  DEPT+ L   E ++L R IS L+ EG  
Sbjct: 135 HPSTKVRELSIGQQQMIEIGRALLRNARIIAFDEPTSSLSVQETRQLKRIISRLREEGRV 194

Query: 203 FLFISHHLQEVYEICQAVTVLRDARHI-VSAPVSALPREQLIEAMTG-ERGGLAVADAAA 260
            L+++H ++EV+++C AVTV RD +HI   A ++AL  + L+  M G +   +       
Sbjct: 195 VLYVTHRMEEVFDMCDAVTVFRDGKHIRTHASLAALDHDTLVSEMVGRDIEDVYGYRERE 254

Query: 261 RGALPADTAVALELKELTGADYEG-VSFTVKRGEVVGLTGATSSGRTSVAEAIAGLRAAK 319
           RG       V LE+  + G   +  VSF V+RGEV GL G   +GR+ +   + G   A 
Sbjct: 255 RG------EVILEIDAIEGRGLKAPVSFEVRRGEVFGLFGLVGAGRSELMRLVCGAERAS 308

Query: 320 RGTISVDGAILPPGDVPASLAHGIGCVPKDRHHEGLVLTQSVAENASMTIARVLGKFGIA 379
            G +   G          ++  GI   P+DR  +G+    SVA+N +++  R   ++G+ 
Sbjct: 309 AGEVRFQGQARRFASPGEAIRMGIAMCPEDRKSQGIFPVASVADNLNISCRRFFRRWGVL 368

Query: 380 APAKK-NAFGQKMIDALGIVAQGPEHVVSGLSGGNQQKVVMARALATNPNVLVLIDPTAG 438
              ++  A  +  I  L I   GP   +  LSGGNQQKV++AR LA    + V+ +PT G
Sbjct: 369 RDTRRERANAEAYIQRLSIKTPGPRTAIGTLSGGNQQKVILARWLAEKIELFVVDEPTRG 428

Query: 439 VDVKSKEALLSVVDRVREEGKAVLVVSGELDDLRT-CDRVLVMFRGRVAAEFP 490
           +DV ++  + +++  + E+GK+V+V+S +L ++ + CDR+ VM  G +    P
Sbjct: 429 IDVGARRDIYTLLFDLTEQGKSVVVISSDLAEVSSICDRIGVMRDGALVEVVP 481



 Score = 79.7 bits (195), Expect = 2e-19
 Identities = 68/218 (31%), Positives = 104/218 (47%), Gaps = 7/218 (3%)

Query: 33  VSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPDTGEVRFSGAAAPSIADRDAWRERVA 92
           VS  V  GE   L G  GAG+S L+ ++ G  +   GEVRF G A    +  +A R  +A
Sbjct: 274 VSFEVRRGEVFGLFGLVGAGRSELMRLVCGAERASAGEVRFQGQARRFASPGEAIRMGIA 333

Query: 93  -CVYQHST--IIRDLSVAENLFINRQPL--RGGVI-DWQAMRRDARALLDHWKIDVREDA 146
            C     +  I    SVA+NL I+ +    R GV+ D +  R +A A +    I      
Sbjct: 334 MCPEDRKSQGIFPVASVADNLNISCRRFFRRWGVLRDTRRERANAEAYIQRLSIKTPGPR 393

Query: 147 RA-GDLSVEARQLVEIARALSYGARFIILDEPTAQLDGDEIKRLFRRISELQREGVTFLF 205
            A G LS   +Q V +AR L+      ++DEPT  +D    + ++  + +L  +G + + 
Sbjct: 394 TAIGTLSGGNQQKVILARWLAEKIELFVVDEPTRGIDVGARRDIYTLLFDLTEQGKSVVV 453

Query: 206 ISHHLQEVYEICQAVTVLRDARHIVSAPVSALPREQLI 243
           IS  L EV  IC  + V+RD   +   P     +E+L+
Sbjct: 454 ISSDLAEVSSICDRIGVMRDGALVEVVPRHEATQERLL 491


Lambda     K      H
   0.318    0.134    0.377 

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: 623
Number of extensions: 29
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: 510
Length of database: 497
Length adjustment: 34
Effective length of query: 476
Effective length of database: 463
Effective search space:   220388
Effective search space used:   220388
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 24 2021. 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 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