Alignments for a candidate for PS417_11890 in Pseudovibrio axinellae Ad2

GapMind for catabolism of small carbon sources

Alignments for a candidate for PS417_11890 in Pseudovibrio axinellae Ad2

Align Inositol transport system ATP-binding protein (characterized)
to candidate WP_068009665.1 PsAD2_RS19320 ATP-binding cassette domain-containing protein

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



>NCBI__GCF_001623255.1:WP_068009665.1
          Length = 497

 Score =  421 bits (1081), Expect = e-122
 Identities = 216/489 (44%), Positives = 319/489 (65%), Gaps = 3/489 (0%)

Query: 23  LLEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEIRL 82
           LLE+  I K F G+  L  V L +R G V+AL GENGAGKSTLMKII+GIYQ DAG +  
Sbjct: 4   LLELQGIEKSFSGINVLKSVDLTIRAGRVVALAGENGAGKSTLMKIISGIYQRDAGTVFY 63

Query: 83  RGKPIVFETPLAAQKAGIAMIHQELNLMPHMSIAENIWIGREQLNSLHMVNHREMHRCTA 142
           +G  + F     +  AGI +IHQELNL+P +S+AENI++GRE    L  +    + R + 
Sbjct: 64  KGHEVEFTNARESMDAGIGIIHQELNLLPDLSVAENIYLGREP-TKLGKIQWDVVQRESK 122

Query: 143 ELLARLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHLFSI 202
           + LA+L+ ++DP   +G LSIA++QMVEIAKA+S +++++IMDEPT A+T+ E A LF +
Sbjct: 123 KYLAQLKQDIDPTTPLGKLSIAQQQMVEIAKALSLNAEVIIMDEPTDALTDIETAILFEV 182

Query: 203 IADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLISMMVGRELS 262
           + +L++QGKG+V+I+H++ E+F + D++A+ RDG  +       ++ D LI  MVGRELS
Sbjct: 183 VDELRAQGKGLVFISHRLGEIFQMCDDIAILRDGQMVHQGAVADISEDDLIRHMVGRELS 242

Query: 263 QLFPLRETPIGDLLLTVRDLTLDGVFKDVSFDLHAGEILGIAGLMGSGRTNVAETIFGIT 322
             +P      GD+ + V  LT  G  K++SF  +AGE++G AGL+G+GRT +A+ IFG  
Sbjct: 243 DQYPFVPAEPGDVRIEVDKLTARGA-KEISFTANAGEVVGFAGLVGAGRTELAKAIFGAN 301

Query: 323 PSSSGQITLDGKAVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHYTGN 382
           P   G + +DG+ + +  P   ++     +TEDRK  GL    S+  NM +  L  +   
Sbjct: 302 PIRGGSVKIDGQEISLKSPQDGVKAKIGYVTEDRKQEGLVQSQSLGSNMSLTGLDRFCNT 361

Query: 383 -GFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRLLILDEP 441
            G + + +      +  +   +KT      I  LSGGNQQK  +A+ L+  P +LILDEP
Sbjct: 362 LGIVNKTSEAVTISEYIEAFAIKTRDASTIISNLSGGNQQKVSIAKSLVPEPEVLILDEP 421

Query: 442 TRGIDVGAKAEIYRLIAFLASEGMAVIMISSELPEVLGMSDRVMVMHEGELMGTLDRSEA 501
           TRG+DVGAK EIY LI  L +EG+ +++ISS++PE+LG+SDR++V+ +G+L G+ DR EA
Sbjct: 422 TRGVDVGAKREIYTLINKLKAEGLCILLISSDMPELLGISDRILVLSDGKLTGSFDRDEA 481

Query: 502 TQEKVMQLA 510
           TQE +M+ A
Sbjct: 482 TQENIMRCA 490



 Score = 80.5 bits (197), Expect = 1e-19
 Identities = 58/223 (26%), Positives = 106/223 (47%), Gaps = 6/223 (2%)

Query: 41  DVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEIRLRGKPIVFETPLAAQKAGI 100
           ++      G V+   G  GAG++ L K I G      G +++ G+ I  ++P    KA I
Sbjct: 269 EISFTANAGEVVGFAGLVGAGRTELAKAIFGANPIRGGSVKIDGQEISLKSPQDGVKAKI 328

Query: 101 AMIHQELN---LMPHMSIAENIWI-GREQL-NSLHMVNHREMHRCTAELLARLRINL-DP 154
             + ++     L+   S+  N+ + G ++  N+L +VN        +E +    I   D 
Sbjct: 329 GYVTEDRKQEGLVQSQSLGSNMSLTGLDRFCNTLGIVNKTSEAVTISEYIEAFAIKTRDA 388

Query: 155 EEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHLFSIIADLKSQGKGIV 214
              + NLS   +Q V IAK++  + ++LI+DEPT  +       ++++I  LK++G  I+
Sbjct: 389 STIISNLSGGNQQKVSIAKSLVPEPEVLILDEPTRGVDVGAKREIYTLINKLKAEGLCIL 448

Query: 215 YITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLISMMV 257
            I+  M E+  I+D + V  DG   G    D    ++++   V
Sbjct: 449 LISSDMPELLGISDRILVLSDGKLTGSFDRDEATQENIMRCAV 491


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: 606
Number of extensions: 35
Number of successful extensions: 7
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: 497
Length adjustment: 34
Effective length of query: 483
Effective length of database: 463
Effective search space:   223629
Effective search space used:   223629
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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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