GapMind for catabolism of small carbon sources

 

Aligments for a candidate for malK1 in Herbaspirillum seropedicae SmR1

Align MalK; aka Sugar ABC transporter, ATP-binding protein, component of The maltose, maltotriose, mannotetraose (MalE1)/maltose, maltotriose, trehalose (MalE2) porter (Nanavati et al., 2005). For MalG1 (823aas) and MalG2 (833aas), the C-terminal transmembrane domain with 6 putative TMSs is preceded by a single N-terminal TMS and a large (600 residue) hydrophilic region showing sequence similarity to MLP1 and 2 (9.A.14; e-12 & e-7) as well as other proteins (characterized)
to candidate HSERO_RS22750 HSERO_RS22750 sugar ABC transporter ATP-binding protein

Query= TCDB::Q9X103
         (369 letters)



>lcl|FitnessBrowser__HerbieS:HSERO_RS22750 HSERO_RS22750 sugar ABC
           transporter ATP-binding protein
          Length = 377

 Score =  330 bits (846), Expect = 4e-95
 Identities = 187/365 (51%), Positives = 239/365 (65%), Gaps = 13/365 (3%)

Query: 3   MAQVVLENVTKVYENKVVAVKNANLVVEDKEFVVLLGPSGCGKTTTLRMIAGLEEITDGK 62
           MA V ++ + K Y+ +   +   NL + D EF VL+GPSGCGK+T LRM+ GLEEI+ G+
Sbjct: 1   MAHVNIKQLRKTYDGRADVLAGLNLDIRDGEFCVLVGPSGCGKSTLLRMLCGLEEISGGE 60

Query: 63  IYIDGKVVNDVEPKDRDIAMVFQNYALYPHMTVYENMAFGLKLRKYPKDEIDRRVREAAK 122
           + I G+VVN + P +R IAMVFQ+YALYPHM VY+NMAFGLK+    K +ID R+R AA 
Sbjct: 61  LAIGGQVVNHLPPAERGIAMVFQSYALYPHMNVYKNMAFGLKVAGNSKSDIDARIRHAAA 120

Query: 123 ILGIENLLDRKPRQLSGGQRQRVAVGRAIVRNPKVFLFDEPLSNLDAKLRVQMRSELKKL 182
           IL I++LL R PR+LSGGQRQRVA+GRAIVR P++FLFDEPLSNLDA LRVQ R E+ KL
Sbjct: 121 ILKIDHLLQRLPRELSGGQRQRVAIGRAIVRQPRLFLFDEPLSNLDAALRVQTRLEIAKL 180

Query: 183 HHRLQATIIYVTHDQVEAMTMADKIVVMKDGEIQQIGTPHEIYNSPANVFVAGFIGSPPM 242
           H +L ATI+YVTHDQVEAMT+ DKIVVM +G IQQ GTP E+Y  P N+FVAGFIGSP M
Sbjct: 181 HRQLAATIVYVTHDQVEAMTLGDKIVVMHEGRIQQAGTPLELYQQPQNLFVAGFIGSPKM 240

Query: 243 NFVNARVVR-GEGGLWIQ-ASGFKVKVPKEFEDKLANYIDKEIIFGIRPEDIYDKLFALA 300
           NF    V R  + G+ ++ A G ++       D L       +  G+R E I + L    
Sbjct: 241 NFFQGVVTRCDDSGVQVEIAGGLRLLAD---VDPLGVTPGAAVTLGLRAEQIREGLGDGQ 297

Query: 301 PSPENTITGVVDVVEPLGSETILHVKV--GDDLIVASVNPRTQAKEEQKIDLVLDMTRMH 358
           P     + GVV++VE LG    L+V +  G D++V     R      Q I L +     H
Sbjct: 298 P-----LHGVVNLVEHLGEANFLYVTLDGGHDIVVRGDGNR-NVDIGQPIALSVHSHAFH 351

Query: 359 AFDKE 363
            FD +
Sbjct: 352 LFDAQ 356


Lambda     K      H
   0.319    0.138    0.387 

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: 365
Number of extensions: 9
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: 369
Length of database: 377
Length adjustment: 30
Effective length of query: 339
Effective length of database: 347
Effective search space:   117633
Effective search space used:   117633
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 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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