GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK_Aa in Alicycliphilus denitrificans K601

Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate WP_013723230.1 ALIDE2_RS22605 putative 2-aminoethylphosphonate ABC transporter ATP-binding protein

Query= BRENDA::Q70HW1
         (384 letters)



>NCBI__GCF_000204645.1:WP_013723230.1
          Length = 377

 Score =  225 bits (573), Expect = 2e-63
 Identities = 135/354 (38%), Positives = 208/354 (58%), Gaps = 17/354 (4%)

Query: 21  VKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEGNLYIGDRRVNDVPPKDRDIA 80
           ++D +L ++  E   F+GPSGCGKTT LR+IAGLE  T G++    R ++ +P  +RD  
Sbjct: 35  LRDIDLTVRQGEMLCFLGPSGCGKTTLLRIIAGLETQTSGSIVQSGRDISWLPASERDYG 94

Query: 81  MVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAAKILDIAHLLDRKPKALSGGQ 140
           +VFQ+YAL+P++T+ +N+A+GL   K+ KAEI  RV E   +  +     + P  LSGGQ
Sbjct: 95  IVFQSYALFPNLTIAENVAYGLVNGKMRKAEIQARVAELLAMAGLPTAGGKYPSQLSGGQ 154

Query: 141 RQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRKLHQRLQTTVIYVTHDQTEAM 200
           +QRVAL RA+   P + L+DEPLS LDA +RV++RAEIR+L +++  T I VTHDQ EA+
Sbjct: 155 QQRVALARALATNPGLLLLDEPLSALDATVRVRLRAEIRRLQKQVGITTIMVTHDQEEAL 214

Query: 201 TMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIGSPAMNFIRGEIVQDGDAFYFRAP 260
           +M DRIVVM  GVI+Q  TP  +Y +P + FVA F+G   +N +RG+ +  G  F     
Sbjct: 215 SMSDRIVVMNHGVIEQVGTPMEIYERPASPFVANFVGK--VNVLRGQAL-GGKRFRVGKM 271

Query: 261 SISLRLPEGRYGVLKASGAIGKPVVLGVRPEDLHDEEVFM-TTYPDSVLQMQVE-----V 314
            I     EG +        +G+ V L +RPED   E +   T Y   VL  +VE      
Sbjct: 272 EIECEASEGSF-------RLGEDVSLYLRPEDRVAEHLEAGTPYRLGVLVNKVEFLGGLC 324

Query: 315 VEHMGSEVYLHTSIGPNTIVARVNPRHVYHVGSSVKLAIDLNKIHIFDAETEES 368
           +  + +E     S+G +  + +++   +   G  + +A+  ++I +F    +++
Sbjct: 325 IAEVSAEALGGQSLGLHFSLNQMHDLGICE-GRRIDIALRASRIRVFSTGRDQA 377


Lambda     K      H
   0.321    0.138    0.395 

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: 345
Number of extensions: 13
Number of successful extensions: 1
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: 384
Length of database: 377
Length adjustment: 30
Effective length of query: 354
Effective length of database: 347
Effective search space:   122838
Effective search space used:   122838
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: 50 (23.9 bits)

This GapMind analysis is from Apr 09 2024. 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