GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlK in Sinorhizobium meliloti 1021

Align ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component (characterized)
to candidate SM_b20002 SM_b20002 sugar ABC transporter ATP-binding protein

Query= reanno::pseudo13_GW456_L13:PfGW456L13_3039
         (367 letters)



>FitnessBrowser__Smeli:SM_b20002
          Length = 358

 Score =  397 bits (1019), Expect = e-115
 Identities = 202/360 (56%), Positives = 264/360 (73%), Gaps = 5/360 (1%)

Query: 1   MANLKIKNLQKGFEGFSIIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSGGTI 60
           M+ L++ +++K + G  +IKG+DL++   EFVVFVGPSGCGKSTLLR+IAGLEE+S G +
Sbjct: 1   MSELQLSDVRKSYGGLEVIKGVDLDIKSGEFVVFVGPSGCGKSTLLRMIAGLEEISSGDL 60

Query: 61  ELDGRDITEVSPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVAKAEVEKKVSEAARI 120
            +D   + +V P+KR +AMVFQ+YALYPHM+VR+NM FAL  AGV +AE+EK+V+EAA I
Sbjct: 61  TIDDVRMNDVDPSKRGIAMVFQSYALYPHMTVRENMGFALRFAGVPRAEIEKRVNEAAHI 120

Query: 121 LELGPMLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELLRLH 180
           LELG +L+RKPKQLSGGQRQRVAIGRAIVR+PKIFLFDEPLSNLDA LRV MR+E+ RLH
Sbjct: 121 LELGALLDRKPKQLSGGQRQRVAIGRAIVRHPKIFLFDEPLSNLDAELRVHMRIEIARLH 180

Query: 181 KELQATMIYVTHDQVEAMTMADKVVVLNGGKIEQVGSPLDLYHQPANLFVAGFLGTPKMG 240
           K+L  T++YVTHDQVEAMT+ADK+VV+  G +EQVGSPLDLY  PANLFVAGF+G+PKM 
Sbjct: 181 KQLATTIVYVTHDQVEAMTLADKIVVMRAGVVEQVGSPLDLYDDPANLFVAGFIGSPKMN 240

Query: 241 FLKGKITRVDSQGCEVQLDAGTRVSLPLGGRHLSVGSAVTLGIRPEHLELAKPGDCALQV 300
           FLKG +  +D      +L       +P+     + G+AVT+GIRPEH + A  G  AL +
Sbjct: 241 FLKG-VIEIDEDQAYARLPDYGDAKIPV-TLQAAAGTAVTIGIRPEHFDEA--GPAALDL 296

Query: 301 TADVSERLGSDTFCHVR-TASGEALTMRVRGDLASRYGETLSLHLDAQHCHLFDADGVAL 359
             D+ E LG +TF + R   +GE + +  +     + G+ L+   D     +FD +G  L
Sbjct: 297 AIDMLEHLGGETFAYARHHGNGELIVVETKNGRGLKTGDRLTARFDPVSVLVFDGEGKRL 356


Lambda     K      H
   0.320    0.137    0.389 

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: 427
Number of extensions: 11
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: 367
Length of database: 358
Length adjustment: 29
Effective length of query: 338
Effective length of database: 329
Effective search space:   111202
Effective search space used:   111202
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