GapMind for catabolism of small carbon sources

 

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

Align MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized)
to candidate Ac3H11_1002 ABC transporter ATP-binding protein

Query= TCDB::Q8DT25
         (377 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1002
          Length = 356

 Score =  217 bits (552), Expect = 5e-61
 Identities = 129/321 (40%), Positives = 192/321 (59%), Gaps = 29/321 (9%)

Query: 11  KRYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEGNLYIDDKLMN 70
           KRY + K  +V+  NL I    +   +GPSGCGKSTTLRMIAG E +T G++ ++++ + 
Sbjct: 20  KRYASGKP-AVDAINLRIASGSYCCLLGPSGCGKSTTLRMIAGHESVTSGDILLENRNIT 78

Query: 71  DASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEAAEILGLTEFLE 130
           D     R  AM+FQ++AL+PH+S  +N+AF LK++   K +   +  +  E + L    E
Sbjct: 79  DLPAAARGTAMMFQSFALFPHLSALDNVAFSLKMKGVPKAERQAKARDLLERVALGHLAE 138

Query: 131 RKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEIAKIHRRIGATTI 190
           RKPA+LSGGQ+QRVA+ RA++   +V L+DEPLS LD  LR+ MRAE+ +  + +G T I
Sbjct: 139 RKPAELSGGQQQRVALARALITQPRVLLLDEPLSALDPFLRIQMRAELRRWQKELGLTFI 198

Query: 191 YVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPANKFVAGFIGSPA 250
           +VTH Q EAM LAD +V+M+           G IEQ+G+P E+YN PA++FVA F+G   
Sbjct: 199 HVTHSQEEAMALADTMVVMNH----------GVIEQVGSPHEVYNRPASEFVARFMG--G 246

Query: 251 MNFFEVTVEKERLVNQDGLSLA-----LPQGQEKIL---EEKGYLGKKVTLGIRPEDISS 302
            N  + T E +  V  D L +A     LP G +++L    +  Y G  V LG++ + ++ 
Sbjct: 247 HNVID-TPEGKVGVRTDHLQIAPASAELPWGAQRMLAVVTDVEYQGTYVLLGLQKQGVAL 305

Query: 303 DQIVHETFPNASVTADILVSE 323
                    NA+    ++VSE
Sbjct: 306 S-------ANATAAYSVMVSE 319


Lambda     K      H
   0.318    0.135    0.379 

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: 262
Number of extensions: 8
Number of successful extensions: 2
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: 377
Length of database: 356
Length adjustment: 30
Effective length of query: 347
Effective length of database: 326
Effective search space:   113122
Effective search space used:   113122
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 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