GapMind for catabolism of small carbon sources

 

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

Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate Ac3H11_2058 Putrescine transport ATP-binding protein PotA (TC 3.A.1.11.1)

Query= BRENDA::Q70HW1
         (384 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2058
          Length = 360

 Score =  234 bits (597), Expect = 3e-66
 Identities = 145/363 (39%), Positives = 207/363 (57%), Gaps = 24/363 (6%)

Query: 2   ARVLLEHIYKTYPGQTEPT--VKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITE 59
           A ++  +I K Y   +     VK  + ++     T  +GPSGCGKTTTLRMIAGLE  T 
Sbjct: 6   AGIVFRNITKRYGTDSSAALAVKGISFEVPRGTLTTILGPSGCGKTTTLRMIAGLESPTS 65

Query: 60  GNLYIGDRRVNDVPPKDRDIAMVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEA 119
           G ++IG + V  + P  R+++M+FQ+YAL+PHM V +N+ +GL++   PK +   +  EA
Sbjct: 66  GEIFIGGKDVTTLGPAQRNVSMMFQSYALFPHMNVVENVMYGLRMSGQPKEQARAKAVEA 125

Query: 120 AKILDIAHLLDRKPKALSGGQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIR 179
            + + +    DR P  LSGGQ+QRVAL RA+V EP+V L DEPLSNLDA+LR +MR EIR
Sbjct: 126 LRGVGLVGFDDRLPSELSGGQQQRVALARALVLEPEVLLFDEPLSNLDARLRREMREEIR 185

Query: 180 KLHQRLQTTVIYVTHDQTEAMTMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIGSP 239
            L QRL  TV YVTHDQ EAM + D+I+VM  G+I Q  +P+ +Y  P + FVAGF+G  
Sbjct: 186 ALQQRLSLTVAYVTHDQAEAMAVSDQIIVMNQGLIAQKGSPRALYETPHSEFVAGFMGE- 244

Query: 240 AMNFIRGEIVQDGDAFYFRAPSISLRLPEGRYGVLKASGAIGKPVVLGVRPEDLHDEEVF 299
           AM F     V D D      P +       R  V   SG    PV + VRPE        
Sbjct: 245 AMLF---PAVADADGTVALGPLVL------RPRVAVKSG----PVKVAVRPEAWR----- 286

Query: 300 MTTYPDSVLQMQVEVVEHMGS--EVYLHTSIGPNTIVARVNPRHVYHVGSSVKLAIDLNK 357
           +T   + +L  ++    ++G+  E    T++G +  V   +   V  VG  V+L + ++ 
Sbjct: 287 ITRQGEGLLPARLAKSAYLGAVHEYTFETALG-SIFVVSSDLDDVLAVGDDVQLGLGVHG 345

Query: 358 IHI 360
           + +
Sbjct: 346 VSV 348


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: 325
Number of extensions: 11
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: 360
Length adjustment: 30
Effective length of query: 354
Effective length of database: 330
Effective search space:   116820
Effective search space used:   116820
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: 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