GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_11890 in Collimonas arenae Ter10

Align m-Inositol ABC transporter, ATPase component (itaA) (characterized)
to candidate WP_061532804.1 CAter10_RS06720 sugar ABC transporter ATP-binding protein

Query= reanno::pseudo3_N2E3:AO353_21385
         (521 letters)



>NCBI__GCF_001584165.1:WP_061532804.1
          Length = 515

 Score =  414 bits (1063), Expect = e-120
 Identities = 226/498 (45%), Positives = 328/498 (65%), Gaps = 9/498 (1%)

Query: 27  LLEIINVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAG-ELR 85
           +LE+  +SK F G+  L +V L V  G V ALMGENGAGKSTLMK+++G +Q D G E+R
Sbjct: 10  ILEMRGISKTFSGLRVLKEVDLTVYAGEVHALMGENGAGKSTLMKVLSGAHQADTGGEIR 69

Query: 86  LRGKPVTFDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNGFHMIDHREMHRCT 145
           + G+ V    P AA + G+A+I+QEL+L P++S+AENI++GRE   G+  +D + M    
Sbjct: 70  IDGRRVVNYGPRAAKEHGVAVIYQELSLCPNLSVAENIYLGRELRQGWS-VDRKAMEAGC 128

Query: 146 AQLLERLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITDKEVAHLFS 205
             +L+RL  +  P  +V +LSIAERQ+VEIA+A+   + IL+MDEPT+ ++ +E   LF+
Sbjct: 129 VDVLKRLGADFTPHTKVSSLSIAERQLVEIARAIHAHARILVMDEPTTPLSSRETDRLFA 188

Query: 206 IIADLKAQGKGIIYITHKMNEVFSIADEVAVFRDGAYIGLQRADSMDGDSLISMMVGREL 265
           +I  L+ +G  I+YI+H+M E++ ++D V+V RDG ++G+   D +  + L+ MMVGR+L
Sbjct: 189 LIRQLREEGLAIVYISHRMAEIYELSDRVSVLRDGKHVGMLERDELSAEVLVKMMVGRDL 248

Query: 266 SQLFPVREKPI--GDLLMSVRDLRLDGVFKGVSFDLHAGEILGIAGLMGSGRTNVAEAIF 323
           S  +     P   G+++M VRD+      +G SFDLHAGE+LGIAGL+G+GRT +A  IF
Sbjct: 249 SGFYKKEHAPYDPGNVVMRVRDMADGRRVRGCSFDLHAGEVLGIAGLVGAGRTELARLIF 308

Query: 324 GITPSDGGEICLDGQPV-RISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEM-AVLP 381
           G  P   G + + GQ V  +  P  AI  G   LTEDRK  GLF  +SV +N+ + A +P
Sbjct: 309 GADPRIAGTLEVAGQAVSNLRGPADAIRAGVVYLTEDRKAQGLFLDMSVRDNINVCACVP 368

Query: 382 HYAGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRILI 441
                G + ++       +  K L ++  S    +  LSGGNQQK LLAR L   P +LI
Sbjct: 369 DAGYGGVLDRRRGAQRAAEAIKSLSIRVASPGVNVGALSGGNQQKVLLARLLEIKPHVLI 428

Query: 442 LDEPTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEGDLMGTL- 500
           LDEPTRG+D+GAK+EIYR+I+ LA+ G+ V++ISSELPE++G SDRV+VM EG+L+  L 
Sbjct: 429 LDEPTRGVDIGAKSEIYRIINELANAGIGVVVISSELPEIVGTSDRVLVMREGELVAELG 488

Query: 501 --DRSEATQERVMQLASG 516
                E TQE +++LA+G
Sbjct: 489 GHSGREITQENIIELATG 506


Lambda     K      H
   0.321    0.137    0.391 

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: 707
Number of extensions: 41
Number of successful extensions: 10
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 521
Length of database: 515
Length adjustment: 35
Effective length of query: 486
Effective length of database: 480
Effective search space:   233280
Effective search space used:   233280
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:

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:

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:

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:

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