GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctM in Sinorhizobium meliloti 1021

Align Putative TRAP dicarboxylate transporter, DctM subunit (characterized, see rationale)
to candidate SMa0250 SMa0250 dedA-like protein

Query= uniprot:Q88NP0
         (426 letters)



>FitnessBrowser__Smeli:SMa0250
          Length = 425

 Score =  310 bits (794), Expect = 5e-89
 Identities = 166/418 (39%), Positives = 260/418 (62%), Gaps = 3/418 (0%)

Query: 1   MEAFILLGSFIVLILIGMPVAYALGLSALIGAWWIDI-PLQAMMIQVASGVNKFSLLAIP 59
           M   + + S +  + IG+PVA++L    ++  W++ +   Q +   + +G + F+LLAIP
Sbjct: 1   MTLVVFIVSLLGAMAIGVPVAFSLMFCGVVLMWYMGMFNTQIIAQNMIAGADTFTLLAIP 60

Query: 60  FFVLAGAIMAEGGMSRRLVAFAGVLVGFVRGGLSLVNIMASTFFGAISGSSVADTASVGS 119
           FF+LAG +M  GG+SRR++ FA   VG +RGGL +V IMA+    +ISGS+ ADTA++ +
Sbjct: 61  FFILAGELMNAGGLSRRIIDFAIACVGHIRGGLGIVAIMAAVIMASISGSAAADTAALAA 120

Query: 120 VLIPEMERKGYPREFSTAVTVSGSVQALLTPPSHNSVLYSLAAGGTVSIASLFMAGIMPG 179
           +LIP M + GY    S  +  +G V A + PPS   +++ +AA   VSI  LFMAGI+PG
Sbjct: 121 ILIPMMAKAGYNVPRSAGLIAAGGVIAPVIPPSMAFIVFGVAAN--VSITQLFMAGIVPG 178

Query: 180 LLLSAVMMGLCLIFAKKRNYPKGEVIPLREALKIAGEALWGLMAMVIILGGILSGVFTAT 239
           L++   ++   L+  +K +       P++E +   G ALW L   VIILGGI +GV T T
Sbjct: 179 LIMGIALVATWLLVVRKDDIQPLPRTPMKERVGATGRALWALGMPVIILGGIKAGVVTPT 238

Query: 240 ESAAVAVVWSFFVTMFIYRDYKWRDLPKLMHRTVRTISIVMILIGFAASFGYVMTLMQIP 299
           E+A VA V++ FV M IYR+ K RDLP ++ +  +T +++M L+  A    +++T   IP
Sbjct: 239 EAAVVAAVYALFVGMVIYRELKPRDLPGVILQAAKTTAVIMFLVCAALVSSWLITAANIP 298

Query: 300 SKITTAFLTLSDNRYVILMCINFMLMLLGTVMDMAPLILILTPILLPVITGIGVDPVHFG 359
           S+IT     L D   +++  I  +++++GT +D+ P ILILTP+L+P+I   G+DPV+FG
Sbjct: 299 SEITGFISPLIDRPTLLMFVIMLVVLVVGTALDLTPTILILTPVLMPIIKQAGIDPVYFG 358

Query: 360 MIMLVNLGIGLITPPVGAVLFVGSAIGKVSIESTVKALMPFYLALFLVLMAVTYIPAI 417
           ++ ++N  IGL+TPPVG VL V S +G+V +   +  + PF +A  LVL  +   P I
Sbjct: 359 VLFIMNTCIGLLTPPVGVVLNVVSGVGRVPLGKVIVGVTPFLVAQILVLFLLVLFPDI 416


Lambda     K      H
   0.329    0.142    0.418 

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: 571
Number of extensions: 35
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: 426
Length of database: 425
Length adjustment: 32
Effective length of query: 394
Effective length of database: 393
Effective search space:   154842
Effective search space used:   154842
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 51 (24.3 bits)

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

Links

Downloads

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:

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