Alignments for a candidate for HSERO_RS05250 in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for HSERO_RS05250 in Pseudomonas simiae WCS417

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate GFF3463 PS417_17730 ribonucleotide-diphosphate reductase subunit alpha

Query= uniprot:D8J111
         (520 letters)



>FitnessBrowser__WCS417:GFF3463
          Length = 502

 Score =  418 bits (1075), Expect = e-121
 Identities = 221/492 (44%), Positives = 322/492 (65%), Gaps = 2/492 (0%)

Query: 22  VIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDILL 81
           ++ L N+CKR+PGV AL +   ++  GE+HAL+GENGAGKSTLMKIL GV  +D G IL+
Sbjct: 4   LLKLENICKRYPGVQALKSINLQVERGEIHALLGENGAGKSTLMKILGGVEHQDEGQILI 63

Query: 82  DGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFIDEDELNRQA 141
           DG+  +    R A A GIGI+ QE +L+ +L+A +NIF+G E     GL + + E+   +
Sbjct: 64  DGQAQQFATYRDAIAAGIGIVFQEFSLIPYLTAVENIFLGHELSNRFGL-LRKREMVEAS 122

Query: 142 AAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAELFR 201
            A+F R+ + +D    V  L+VA QQ VEIAKAL+ D+R+L++DEPTA L  +E   LF 
Sbjct: 123 EALFKRLGVTIDLQCAVKHLSVAEQQFVEIAKALALDARLLVLDEPTATLTPSEAELLFE 182

Query: 202 IIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMVGRAL 261
           I+R+L+ QGV +++ISH ++E+ Q+ DR+SV+RDG  +    + ++ +D ++ MMVGR L
Sbjct: 183 IMRELKRQGVAVIFISHHLEEIFQVCDRISVLRDGGNVGVTDVADSDIDHLVEMMVGRRL 242

Query: 262 DGEQRIPPDTSRNDVVLEVRGLNRGRAIRDVSFTLRKGEILGFAGLMGAGRTEVARAIFG 321
                  P   R  ++LEV+ +   R      F L KGEILGFAGL+G+GRTE+A  + G
Sbjct: 243 ACSFPPKPTRERGPLLLEVKDIQLVRNGPHNRFQLHKGEILGFAGLVGSGRTELALGMMG 302

Query: 322 ADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSSMGRFT 381
           A P  + ++ + G K  +  PA A+AHGIG L E RK  GL     ++ NI+L+++ ++ 
Sbjct: 303 ALPSVSKDVWLRGEKITLDDPAQALAHGIGLLPESRKSEGLITDFSIRENISLNNLPKYQ 362

Query: 382 RV-GFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLRDCDILFFD 440
              G +D+     + +  ++QL+IK PS E +   LSGGNQQK+VIA+W+   CD+L FD
Sbjct: 363 NASGLIDKNRECASVEGLMKQLSIKAPSSESRVFNLSGGNQQKVVIARWINHHCDVLVFD 422

Query: 441 EPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITGELARA 500
           EPTRGIDVGAK++IY L+ +L EQG AI+MISSELPE++ M  RV V  +G I   L  +
Sbjct: 423 EPTRGIDVGAKAQIYALMRSLTEQGYAIIMISSELPEIIGMCDRVAVFHKGAIVKLLEAS 482

Query: 501 DATQEKIMQLAT 512
               +++M+ AT
Sbjct: 483 AVNPQEVMRHAT 494



 Score = 89.4 bits (220), Expect = 3e-22
 Identities = 61/231 (26%), Positives = 116/231 (50%), Gaps = 5/231 (2%)

Query: 287 RAIRDVSFTLRKGEILGFAGLMGAGRTEVARAIFGADPLEAGEIIIHGGKAVIKSPADAV 346
           +A++ ++  + +GEI    G  GAG++ + + + G +  + G+I+I G      +  DA+
Sbjct: 18  QALKSINLQVERGEIHALLGENGAGKSTLMKILGGVEHQDEGQILIDGQAQQFATYRDAI 77

Query: 347 AHGIGYLSEDRKHFGLAVGMDVQANIALSSMGRFTRVGFMDQRAIREAAQMYVRQLAIKT 406
           A GIG + ++   F L   +    NI L       R G + +R + EA++   ++L + T
Sbjct: 78  AAGIGIVFQE---FSLIPYLTAVENIFLGHE-LSNRFGLLRKREMVEASEALFKRLGV-T 132

Query: 407 PSVEQQARLLSGGNQQKIVIAKWLLRDCDILFFDEPTRGIDVGAKSEIYKLLDALAEQGK 466
             ++   + LS   QQ + IAK L  D  +L  DEPT  +       +++++  L  QG 
Sbjct: 133 IDLQCAVKHLSVAEQQFVEIAKALALDARLLVLDEPTATLTPSEAELLFEIMRELKRQGV 192

Query: 467 AIVMISSELPEVLRMSHRVLVMCEGRITGELARADATQEKIMQLATQRESA 517
           A++ IS  L E+ ++  R+ V+ +G   G    AD+  + ++++   R  A
Sbjct: 193 AVIFISHHLEEIFQVCDRISVLRDGGNVGVTDVADSDIDHLVEMMVGRRLA 243


Lambda     K      H
   0.320    0.135    0.372 

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: 593
Number of extensions: 27
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: 520
Length of database: 502
Length adjustment: 35
Effective length of query: 485
Effective length of database: 467
Effective search space:   226495
Effective search space used:   226495
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