Alignments for a candidate for PS417_11890 in Moritella dasanensis ArB 0140

GapMind for catabolism of small carbon sources

Alignments for a candidate for PS417_11890 in Moritella dasanensis ArB 0140

Align Inositol transport system ATP-binding protein (characterized)
to candidate WP_017221119.1 A923_RS0107850 ribose ABC transporter ATP-binding protein RbsA

Query= reanno::WCS417:GFF2332
         (517 letters)



>NCBI__GCF_000276805.1:WP_017221119.1
          Length = 501

 Score =  451 bits (1160), Expect = e-131
 Identities = 233/490 (47%), Positives = 321/490 (65%), Gaps = 1/490 (0%)

Query: 23  LLEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEIRL 82
           +L++  I K FPGV AL +  L V PG V+AL+GENGAGKSTLMK++ GIY  D G I  
Sbjct: 5   ILKLSGIEKSFPGVKALDNACLNVYPGKVMALLGENGAGKSTLMKVLTGIYHMDKGSINY 64

Query: 83  RGKPIVFETPLAAQKAGIAMIHQELNLMPHMSIAENIWIGREQLNSLHMVNHREMHRCTA 142
           +G  + F+ P  +Q+ GI++IHQELNL+P ++IAENI++GRE  N+   +   +M     
Sbjct: 65  QGSDVTFDGPRHSQEVGISIIHQELNLIPELTIAENIYLGRETTNAFGGIKWTQMFADAD 124

Query: 143 ELLARLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHLFSI 202
            LL RL +     + +G LS+ E+QMVEIAKA+S+ S +++MDEPT A+TE E   LF +
Sbjct: 125 ALLQRLNVKHSSRQLLGELSLGEQQMVEIAKALSFKSQVIVMDEPTDALTESETKSLFKV 184

Query: 203 IADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLISMMVGRELS 262
           I +L+++G GIVYI+H++ E+F I D++ V RDG +I       ++ D LI  MVGR L 
Sbjct: 185 INELRNEGCGIVYISHRLKEIFEICDDITVLRDGKFIAEIAVTDIDEDGLIEKMVGRRLD 244

Query: 263 QLFPLRETPIGDLLLTVRDLTLDGVFKDVSFDLHAGEILGIAGLMGSGRTNVAETIFGIT 322
           +++P  +   G L L V ++   GV +DVSF L  GEILGI+GLMG+GRT + + I+G  
Sbjct: 245 EIYPRIDAKHGTLCLEVENIVAPGV-RDVSFTLDHGEILGISGLMGAGRTELMKAIYGAL 303

Query: 323 PSSSGQITLDGKAVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHYTGN 382
           P  SG + LD K V    P   +  G A ++EDRK  GL   LSV ENM +  L   +  
Sbjct: 304 PRQSGDVILDDKVVSPITPRDGLANGIAYISEDRKGDGLILGLSVKENMSLCALDALSKG 363

Query: 383 GFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRLLILDEPT 442
             +         ED  ++  VKTPS +Q I  LSGGNQQK  +A+ LMT P++LILDEPT
Sbjct: 364 LQLDHAKEATAVEDFMRQFNVKTPSRDQIIGNLSGGNQQKVAIAKGLMTRPKVLILDEPT 423

Query: 443 RGIDVGAKAEIYRLIAFLASEGMAVIMISSELPEVLGMSDRVMVMHEGELMGTLDRSEAT 502
           RG+DVGAK EIY+LI    +EGM++I++SSE+PEVLGMSDR++VMHEG + G    ++A 
Sbjct: 424 RGVDVGAKKEIYQLINQFKAEGMSIILVSSEMPEVLGMSDRILVMHEGRISGEFMAADAN 483

Query: 503 QEKVMQLASG 512
           QEK+M  A G
Sbjct: 484 QEKLMACAVG 493



 Score = 95.9 bits (237), Expect = 3e-24
 Identities = 67/245 (27%), Positives = 121/245 (49%), Gaps = 10/245 (4%)

Query: 24  LEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEIRLR 83
           LE+ NI    PGV    DV   +  G +L + G  GAG++ LMK I G     +G++ L 
Sbjct: 259 LEVENIVA--PGV---RDVSFTLDHGEILGISGLMGAGRTELMKAIYGALPRQSGDVILD 313

Query: 84  GKPIVFETPLAAQKAGIAMIHQELN---LMPHMSIAENIWI-GREQLNSLHMVNHREMHR 139
            K +   TP      GIA I ++     L+  +S+ EN+ +   + L+    ++H +   
Sbjct: 314 DKVVSPITPRDGLANGIAYISEDRKGDGLILGLSVKENMSLCALDALSKGLQLDHAKEAT 373

Query: 140 CTAELLARLRINLDPEEQV-GNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAH 198
              + + +  +     +Q+ GNLS   +Q V IAK +     +LI+DEPT  +       
Sbjct: 374 AVEDFMRQFNVKTPSRDQIIGNLSGGNQQKVAIAKGLMTRPKVLILDEPTRGVDVGAKKE 433

Query: 199 LFSIIADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLISMMVG 258
           ++ +I   K++G  I+ ++ +M EV  ++D + V  +G   G   A   N + L++  VG
Sbjct: 434 IYQLINQFKAEGMSIILVSSEMPEVLGMSDRILVMHEGRISGEFMAADANQEKLMACAVG 493

Query: 259 RELSQ 263
           +++++
Sbjct: 494 KKINE 498


Lambda     K      H
   0.320    0.136    0.381 

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: 628
Number of extensions: 28
Number of successful extensions: 6
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: 517
Length of database: 501
Length adjustment: 34
Effective length of query: 483
Effective length of database: 467
Effective search space:   225561
Effective search space used:   225561
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 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 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