Alignments for a candidate for malK_Ss in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for malK_Ss in Cupriavidus basilensis 4G11

Align MalK, component of Maltose and maltooligosaccharide porter (characterized)
to candidate RR42_RS18195 RR42_RS18195 methionine ABC transporter ATP-binding protein

Query= TCDB::Q97UG5
         (617 letters)



>FitnessBrowser__Cup4G11:RR42_RS18195
          Length = 332

 Score =  216 bits (550), Expect = 1e-60
 Identities = 125/319 (39%), Positives = 185/319 (57%), Gaps = 10/319 (3%)

Query: 9   LKVNELTAGYFNQDGFVIGVTNVNFEVYPNEIFAIAGESGCGKSTLAMAIYGLLKYPGVV 68
           L V  L   +F + G    V +V+F V   EI  + GESG GKS    +I GL+  PG V
Sbjct: 6   LVVEGLKTQFFTRGGVARAVDDVSFSVGRGEIMGLVGESGSGKSMTGYSIMGLIDPPGKV 65

Query: 69  LRGHVYLKDKD-----ILSITQEELRKLRMKEFVYVPQFAMDALDPVAKIGDQMMRAAVS 123
           + G + L  +D     + ++T  ++R +R      + Q  M  L+PV +I  QM+ A ++
Sbjct: 66  VDGRIELTSRDGVTRDLRNLTPAQMRDVRGNRIAMIFQDPMMTLNPVLRIDTQMIEAVLA 125

Query: 124 HG-VNVEEARKLIKEKLELVDLPY--NVVNMYPHELSGGMRQRVVIATSILLNPSLIILD 180
           H  V+   AR+  +  L  V +P     +  YPH+ SGGMRQRV IA ++L  P LII D
Sbjct: 126 HEKVDKAVARERSRNALARVGIPSPDERLRAYPHQFSGGMRQRVAIAIALLNKPDLIIAD 185

Query: 181 EPTTGLDVIVQYEILKDLKRIQRQLGVSLVIISHDISMLLMISDRVGIMYAGEIVEIGSK 240
           EPTT LDV +Q +IL +++++ R+ G +L+ I+HD+S++  ++D V +MYAG+IVE G  
Sbjct: 186 EPTTALDVTIQGQILYEMQKLCRESGTALIWITHDLSVVAGLADTVCVMYAGKIVEAGDV 245

Query: 241 EEIIKRPSHPYTYLLISSLPSLVKRREKLLSIPGNPPLMLSKVPNSCRFYDRCPFKMEKC 300
            ++++RP HPYT+ LISS PS   R   L  IPG  P +L+ +P  C F +RC +  + C
Sbjct: 246 RQVLERPEHPYTHGLISSAPSRNPRGAPLRQIPGMTPSLLN-LPAGCAFRERCTYATDVC 304

Query: 301 STLNPALGDIMDGHKARCF 319
            T  P L    DG + RCF
Sbjct: 305 KTA-PPLDTAADGRRLRCF 322



 Score =  147 bits (372), Expect = 5e-40
 Identities = 89/243 (36%), Positives = 138/243 (56%), Gaps = 12/243 (4%)

Query: 380 AVNDVSFELKKGTITALVGGSGHGKSTIAKILAGMIQQ----TSGKIILLGKDVSEYGVR 435
           AV+DVSF + +G I  LVG SG GKS     + G+I        G+I L  +D     +R
Sbjct: 24  AVDDVSFSVGRGEIMGLVGESGSGKSMTGYSIMGLIDPPGKVVDGRIELTSRDGVTRDLR 83

Query: 436 NSMWYK------ENVQMIFQDPYSSLDPRHTVRWHVERPLLIHKKVSNKDQLLPKIIEVL 489
           N    +        + MIFQDP  +L+P   +   +   +L H+KV +K     +    L
Sbjct: 84  NLTPAQMRDVRGNRIAMIFQDPMMTLNPVLRIDTQMIEAVLAHEKV-DKAVARERSRNAL 142

Query: 490 KNVGLKPPEKYLYKYPHELSGGERQRVAIARATAVEPKVLVADEPVSMLDASLRAGILNL 549
             VG+  P++ L  YPH+ SGG RQRVAIA A   +P +++ADEP + LD +++  IL  
Sbjct: 143 ARVGIPSPDERLRAYPHQFSGGMRQRVAIAIALLNKPDLIIADEPTTALDVTIQGQILYE 202

Query: 550 IKKF-KKNGISILYITHDIATVNYIADEIMVIYKGRIVEKGNTYEVISNPSHEYTKRLIE 608
           ++K  +++G ++++ITHD++ V  +AD + V+Y G+IVE G+  +V+  P H YT  LI 
Sbjct: 203 MQKLCRESGTALIWITHDLSVVAGLADTVCVMYAGKIVEAGDVRQVLERPEHPYTHGLIS 262

Query: 609 AVP 611
           + P
Sbjct: 263 SAP 265


Lambda     K      H
   0.319    0.138    0.391 

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: 489
Number of extensions: 23
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 617
Length of database: 332
Length adjustment: 33
Effective length of query: 584
Effective length of database: 299
Effective search space:   174616
Effective search space used:   174616
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 (21.7 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources