Alignments for a candidate for BPHYT_RS16930 in Pseudomonas stutzeri RCH2

GapMind for catabolism of small carbon sources

Alignments for a candidate for BPHYT_RS16930 in Pseudomonas stutzeri RCH2

Align Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale)
to candidate GFF1357 Psest_1392 ABC-type uncharacterized transport systems, ATPase components

Query= uniprot:B2SYR5
         (512 letters)



>FitnessBrowser__psRCH2:GFF1357
          Length = 518

 Score =  237 bits (604), Expect = 9e-67
 Identities = 161/493 (32%), Positives = 253/493 (51%), Gaps = 31/493 (6%)

Query: 2   SATLRFDNIGKVFPGVRALDGVSFDVNVGQVHGLMGENGAGKSTLLKILGGEYQPDSGRV 61
           +A L+   I K +PG  A D +   +  G++H L+GENGAGKSTL+KI+ G  QPD+G +
Sbjct: 6   TARLQLCGITKQYPGCLANDRIDLSIQPGEIHALLGENGAGKSTLMKIIYGVTQPDAGEI 65

Query: 62  MIDGNEVRFTSAASSIAAGIAVIHQELQYVPDLTVAENLLLGQLPNSLGWVNKREAKRFV 121
              G  V     A +   GI ++ Q       L+VAEN+ L  L    G   + E K  +
Sbjct: 66  HWQGERVTMRDPAQARERGIGMVFQHFSLFETLSVAENIALA-LGAKAGTPKQLEPK--I 122

Query: 122 RERLEAMGVALDPNAKLRKLSIAQRQMVEICKALLRNARVIALDEPTSSLSHRETEVLFK 181
           RE  +  G+ L+P   +  LSI +RQ VEI + L+++ R++ LDEPTS L+ +E + LF 
Sbjct: 123 REVSQRYGMPLEPQRLVHSLSIGERQRVEIIRCLMQDIRLLILDEPTSVLTPQEADELFV 182

Query: 182 LVRDLRADNRAMIYISHRMDEIYELCDACTIFRDGRKIASHPTLEGVTRDTIVSEMVGRE 241
            +R L A+  ++++ISH+++E+  LC + T+ R GR        E +  +    E+    
Sbjct: 183 TLRRLAAEGCSILFISHKLNEVRALCQSATVLRAGRVSG-----ECIPAECSDLELARLM 237

Query: 242 ISDIYNYSAR-PLGEVRFAAKGIE----------GHALAQPASFEVRRGEIVGFFGLVGA 290
           + D     A  P  E R     +E          G +L +    EVR GEIVG  G+ G 
Sbjct: 238 VGDAEGLEAEYPKSEGRAPFLRVERLSWHNADPFGVSLKE-VDLEVRAGEIVGIAGVAGN 296

Query: 291 GRSELMHLVYGADHKKGGELL---LDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMAT 347
           G+ EL+ L+ G    +  + +     G  +     G   RHG+   P +R   G V   +
Sbjct: 297 GQDELLALLSGEQRLQAAQAMRIRFLGDDVAHLRPGARRRHGMAFVPAERLGHGAVPSMS 356

Query: 348 VSENINISCRRHYLRVGM----FLDRKKEAETADRFIKLLKIKTPSRRQKIRFLSGGNQQ 403
           +++N  ++    Y + GM     + R +    A++ I+   +KTP  +     LSGGN Q
Sbjct: 357 LADNGLLTA---YQQTGMVEQGLIRRGRVRAFAEQVIQRFAVKTPDAQTPAASLSGGNLQ 413

Query: 404 KAILSRWLAEPDLKVVILDEPTRGIDVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGV 463
           K IL R + +   K++I   PT G+DVGA   I+  + +L + G AI++IS +L E+  +
Sbjct: 414 KFILGREILQQP-KLLIAAHPTWGVDVGAAAAIHRALIELRDAGAAILVISEDLEELFQI 472

Query: 464 SDRIVVMRQGRIS 476
           SDRI  +  GR+S
Sbjct: 473 SDRIAALSDGRLS 485



 Score = 82.0 bits (201), Expect = 5e-20
 Identities = 59/217 (27%), Positives = 105/217 (48%), Gaps = 11/217 (5%)

Query: 276 VRRGEIVGFFGLVGAGRSELMHLVYGADHKKGGELLLDGKPIKVRSAGEAIRHGIVLCPE 335
           ++ GEI    G  GAG+S LM ++YG      GE+   G+ + +R   +A   GI +  +
Sbjct: 31  IQPGEIHALLGENGAGKSTLMKIIYGVTQPDAGEIHWQGERVTMRDPAQARERGIGMVFQ 90

Query: 336 DRKEEGIVAMATVSENINISCRRHYLRVGMFLDRKKEAETADRFIKLLKIKTPSRRQKIR 395
                 +    +V+ENI ++       +G      K+ E   R +          ++ + 
Sbjct: 91  ---HFSLFETLSVAENIALA-------LGAKAGTPKQLEPKIREVSQRYGMPLEPQRLVH 140

Query: 396 FLSGGNQQKAILSRWLAEPDLKVVILDEPTRGIDVGAKHEIYNVIYQLAERGCAIVMISS 455
            LS G +Q+  + R L + D++++ILDEPT  +      E++  + +LA  GC+I+ IS 
Sbjct: 141 SLSIGERQRVEIIRCLMQ-DIRLLILDEPTSVLTPQEADELFVTLRRLAAEGCSILFISH 199

Query: 456 ELPEVLGVSDRIVVMRQGRISGELTRKDATEQSVLSL 492
           +L EV  +     V+R GR+SGE    + ++  +  L
Sbjct: 200 KLNEVRALCQSATVLRAGRVSGECIPAECSDLELARL 236


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: 654
Number of extensions: 31
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: 512
Length of database: 518
Length adjustment: 35
Effective length of query: 477
Effective length of database: 483
Effective search space:   230391
Effective search space used:   230391
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)
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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