GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK in Herbaspirillum seropedicae SmR1

Align ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized)
to candidate HSERO_RS02210 HSERO_RS02210 sugar ABC transporter ATP-binding protein

Query= BRENDA::P68187
         (371 letters)



>FitnessBrowser__HerbieS:HSERO_RS02210
          Length = 372

 Score =  396 bits (1018), Expect = e-115
 Identities = 205/365 (56%), Positives = 258/365 (70%), Gaps = 3/365 (0%)

Query: 1   MASVQLQNVTKAWGEVVVSKDINLDIHEGEFVVFVGPSGCGKSTLLRMIAGLETITSGDL 60
           MA+V ++N+ K + +  V +DINL+I +GEFVVFVGPSGCGKSTLLRMIAGLE I+ GDL
Sbjct: 1   MAAVSIRNLAKRYDDNEVMRDINLEIEDGEFVVFVGPSGCGKSTLLRMIAGLEEISDGDL 60

Query: 61  FIGEKRMNDTPPAERGVGMVFQSYALYPHLSVAENMSFGLKLAGAKKEVINQRVNQVAEV 120
            IG +RMN+ P ++RGV MVFQSYALYPH+S+ +NM+FGLK+AG  K  I+  V   A++
Sbjct: 61  DIGARRMNEVPASKRGVAMVFQSYALYPHMSLYDNMAFGLKIAGKSKAEIDAAVQHAAKI 120

Query: 121 LQLAHLLDRKPKALSGGQRQRVAIGRTLVAEPSVFLLDEPLSNLDAALRVQMRIEISRLH 180
           L + HLLDRKP+ALSGGQRQRVAIGR +  +PSVFL DEPLSNLDAALRV+MR+E ++LH
Sbjct: 121 LHIDHLLDRKPRALSGGQRQRVAIGRAITRQPSVFLFDEPLSNLDAALRVKMRLEFAKLH 180

Query: 181 KRLGRTMIYVTHDQVEAMTLADKIVVLDAGRVAQVGKPLELYHYPADRFVAGFIGSPKMN 240
             L  TMIYVTHDQ+EAMTLADKIVVL  GR+ QVG P +LYH+PA+RFVAGFIGSPKMN
Sbjct: 181 DDLKTTMIYVTHDQIEAMTLADKIVVLSEGRIEQVGSPQQLYHHPANRFVAGFIGSPKMN 240

Query: 241 FLPVKVTATAIDQVQVELPMPNRQQVWLPVESRDVQVGANMSLGIRPEHLLPSDIADVIL 300
           F+   V A   D VQV+LP    Q  W  V+   +QVG  ++LG+RPEHL  +      L
Sbjct: 241 FIDGTVAAIQADGVQVQLPGGGLQ--WAAVDGSTLQVGQKVTLGVRPEHLNIAQ-GQAAL 297

Query: 301 EGEVQVVEQLGNETQIHIQIPSIRQNLVYRQNDVVLVEEGATFAIGLPPERCHLFREDGT 360
           +     +E LG+ + ++         L+ R  D +    G+   +   P RCHLF  DG 
Sbjct: 298 QARCTALELLGDFSYLYAAYEGSEDALILRVPDSLDAPHGSVLPLAADPARCHLFGADGQ 357

Query: 361 ACRRL 365
           A  RL
Sbjct: 358 ALPRL 362


Lambda     K      H
   0.320    0.137    0.393 

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: 395
Number of extensions: 14
Number of successful extensions: 3
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: 371
Length of database: 372
Length adjustment: 30
Effective length of query: 341
Effective length of database: 342
Effective search space:   116622
Effective search space used:   116622
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