Aligments for a candidate for mtlE in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Aligments for a candidate for mtlE in Sinorhizobium meliloti 1021

Align SmoE, component of Hexitol (glucitol; mannitol) porter (characterized)
to candidate SMc01496 SMc01496 sorbitol-binding periplasmic protein

Query= TCDB::O30831
         (436 letters)



>FitnessBrowser__Smeli:SMc01496
          Length = 436

 Score =  711 bits (1834), Expect = 0.0
 Identities = 336/430 (78%), Positives = 382/430 (88%), Gaps = 1/430 (0%)

Query: 8   LMGACAVAALSSAAGAETITVATVNNGDMIRMQGLMSEFNAQHPDITVEWVTLEENVLRQ 67
           L+G C+  AL+  A AET+T+ATVNNGDMIRMQ L  +F +++PDI +EWVTLEENVLRQ
Sbjct: 7   LLGTCSAVALAGLAQAETLTIATVNNGDMIRMQKLTDDFTSKNPDIQLEWVTLEENVLRQ 66

Query: 68  KVTTDIATKGGQFDVLTIGTYEVPIWGKQGWLVSLNDLPPEYDADDILPAIRNGLTVDGE 127
           +VTTDIATKGGQ+D++TIGTYEVPIW KQGWL+ L+DL PEYD DD+LPAIR+GLT+DG+
Sbjct: 67  RVTTDIATKGGQYDIMTIGTYEVPIWAKQGWLLPLDDLGPEYDVDDLLPAIRSGLTIDGK 126

Query: 128 LYAAPFYGESSMIMYRKDLMEKAGLTMPDAPTWDFVKEAAQKMTDKDAEVYGICLRGKAG 187
           LYAAPFYGESSM+MYRKDL EKAGLTMPDAPTWDF+ +AA+K+TDK  E+YGICLRGKAG
Sbjct: 127 LYAAPFYGESSMVMYRKDLFEKAGLTMPDAPTWDFIADAARKITDKGNEIYGICLRGKAG 186

Query: 188 WGENMAFLSAMANSYGARWFDENWQPQFDGEAWKATLTDYLDMMTNYGPPGASKNGFNEN 247
           WGENMAFL+A AN++GARWFDENW+PQFD   WK  L  Y+ +M + GPPGAS NGFNEN
Sbjct: 187 WGENMAFLTATANAFGARWFDENWKPQFDQPEWKNALDFYVKLMNDAGPPGASSNGFNEN 246

Query: 248 LALFQQGKCGMWIDATVAASFVTNPEESTVADKVGFALAPDTGKGKRANWLGAWNLAIPA 307
           L+LFQ GKCGMWIDATVAASFVTNP+ESTVADKVGFALAPDTG GKR NWL AWNLAIPA
Sbjct: 247 LSLFQTGKCGMWIDATVAASFVTNPKESTVADKVGFALAPDTGLGKRGNWLWAWNLAIPA 306

Query: 308 GSQKVDAAKQFIAWATSKDYAELVASKEGWANVPPGTRTSLYENPEYQK-VPFAKMTLDS 366
           GSQK ++A++FIAWAT KDY +LVA KEGWANVPPGTRTSLYENPEYQK  PFAKMTLDS
Sbjct: 307 GSQKAESAQKFIAWATGKDYLKLVAEKEGWANVPPGTRTSLYENPEYQKAAPFAKMTLDS 366

Query: 367 INAADPTHPAVDPVPYVGVQFVAIPEFQGIGTAVGQQFSAALAGSMSAEQALQAAQQFTT 426
           INAADP +PAV PVPYVGVQFVAIPEFQG+GTAVGQ FSAALAG MS +QAL +AQQ +T
Sbjct: 367 INAADPKNPAVKPVPYVGVQFVAIPEFQGLGTAVGQVFSAALAGQMSVDQALASAQQLST 426

Query: 427 REMTRAGYIK 436
           REMT+AGYIK
Sbjct: 427 REMTKAGYIK 436


Lambda     K      H
   0.316    0.131    0.400 

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: 778
Number of extensions: 18
Number of successful extensions: 2
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: 436
Length of database: 436
Length adjustment: 32
Effective length of query: 404
Effective length of database: 404
Effective search space:   163216
Effective search space used:   163216
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 51 (24.3 bits)

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

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

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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:

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, 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

GapMind for catabolism of small carbon sources