GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_11890 in Acidovorax sp. GW101-3H11

Align m-Inositol ABC transporter, ATPase component (itaA) (characterized)
to candidate Ac3H11_609 L-arabinose transport ATP-binding protein AraG (TC 3.A.1.2.2)

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



>FitnessBrowser__acidovorax_3H11:Ac3H11_609
          Length = 505

 Score =  379 bits (974), Expect = e-109
 Identities = 214/501 (42%), Positives = 317/501 (63%), Gaps = 18/501 (3%)

Query: 27  LLEIINVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDA--GEL 84
           LLE+ N+ K FPGVVAL+ V L+V+ G + A++GENGAGKSTLMK+++G+Y   +  G++
Sbjct: 2   LLEMRNIRKTFPGVVALNQVNLQVQAGEIHAIVGENGAGKSTLMKVLSGVYPHGSYSGQI 61

Query: 85  RLRGKPVTFDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNGFHMIDHREMHRC 144
              G+   F     +   GI +IHQEL L+P +SIAENI++G E      +ID    H  
Sbjct: 62  LFDGQEREFAGIRDSEHLGIIIIHQELALVPLLSIAENIFLGNETAR-HGVIDWMAAHSR 120

Query: 145 TAQLLERLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITDKEVAHLF 204
              LL ++ +   P+  VG L + ++Q+VEIAKA+S    +LI+DEPT+++ + +   L 
Sbjct: 121 AQALLHKVGLGESPDTPVGQLGVGKQQLVEIAKALSRKVRLLILDEPTASLNENDSQALL 180

Query: 205 SIIADLKAQGKGIIYITHKMNEVFSIADEVAVFRDGAYIGLQRADSMDG----DSLISMM 260
            ++ +LKAQG   I I+HK+NE+  +AD + V RDG+ +  Q  D  +G    D +I  M
Sbjct: 181 DLLLELKAQGITCILISHKLNEISRVADAITVLRDGSTV--QMLDCREGPVSEDRVIQAM 238

Query: 261 VGRELSQLFPVREKPIGDLLMSVRDLRLDGV-------FKGVSFDLHAGEILGIAGLMGS 313
           VGRE+S  +P R+  +G+++  VR+ R            KG+  ++  GEI+GIAGLMG+
Sbjct: 239 VGREMSDRYPQRQPQVGEIVFEVRNWRAHHPQRSDREHLKGIDLNVRRGEIVGIAGLMGA 298

Query: 314 GRTNVAEAIFGITPSD--GGEICLDGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSV 371
           GRT +A +IFG +      GE+ L GQP+ +S    A+  G A +TEDRK +GL     +
Sbjct: 299 GRTELAMSIFGRSWGQRISGEVRLHGQPIDVSTVEKAVSHGLAYVTEDRKGNGLVLNEDI 358

Query: 372 LENMEMAVLPHYAGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLAR 431
             N  +A LP  +    I       + +D  +KLR++   ++Q    LSGGNQQK +L++
Sbjct: 359 QFNTSLANLPGVSFASVIDSGQEHRVAQDYREKLRIRCSGVDQKTLNLSGGNQQKVVLSK 418

Query: 432 WLMTNPRILILDEPTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVM 491
           WL T+P +LILDEPTRGIDVGAK EIY LI+ LA+EG  VI+ISSE+PE+LG++DR+ VM
Sbjct: 419 WLFTSPEVLILDEPTRGIDVGAKYEIYTLIAQLAAEGKCVIVISSEMPELLGITDRIYVM 478

Query: 492 HEGDLMGTLDRSEATQERVMQ 512
           +EG  +  +  SEA+QE++M+
Sbjct: 479 NEGRFVAEMPTSEASQEKIMR 499


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: 643
Number of extensions: 43
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: 505
Length adjustment: 35
Effective length of query: 486
Effective length of database: 470
Effective search space:   228420
Effective search space used:   228420
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:

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