GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlE in Phyllobacterium brassicacearum STM 196

Align SmoE, component of Hexitol (glucitol; mannitol) porter (characterized)
to candidate WP_106712309.1 CU102_RS17055 sugar ABC transporter substrate-binding protein

Query= TCDB::O30831
         (436 letters)



>NCBI__GCF_003010955.1:WP_106712309.1
          Length = 436

 Score =  640 bits (1651), Expect = 0.0
 Identities = 305/430 (70%), Positives = 356/430 (82%), Gaps = 1/430 (0%)

Query: 8   LMGACAVAALSSAAGAETITVATVNNGDMIRMQGLMSEFNAQHPDITVEWVTLEENVLRQ 67
           L+GA +  AL  AA AET+T+ATVNN DMIRMQ L  +F  ++PDI +EWVTLEENVLRQ
Sbjct: 7   LLGAVSALALGGAAHAETLTIATVNNSDMIRMQKLTEDFTKKNPDIQLEWVTLEENVLRQ 66

Query: 68  KVTTDIATKGGQFDVLTIGTYEVPIWGKQGWLVSLNDLPPEYDADDILPAIRNGLTVDGE 127
           +VTTDIATK GQ+D++TIGTYEVPIW KQGWL+ L+ L   YD  D+LPAI + ++VDG+
Sbjct: 67  RVTTDIATKAGQYDIVTIGTYEVPIWAKQGWLLPLDGLGDSYDKADLLPAISDAVSVDGK 126

Query: 128 LYAAPFYGESSMIMYRKDLMEKAGLTMPDAPTWDFVKEAAQKMTDKDAEVYGICLRGKAG 187
           LYA+PFYGES+M+MYRKDL EKAG+T+P+ PTWD + EAA+KMTDK  E YGICLRGKAG
Sbjct: 127 LYASPFYGESAMVMYRKDLAEKAGVTIPEKPTWDQIAEAAKKMTDKSTETYGICLRGKAG 186

Query: 188 WGENMAFLSAMANSYGARWFDENWQPQFDGEAWKATLTDYLDMMTNYGPPGASKNGFNEN 247
           WGENMA L+A ANSYGARWFDE W PQFD   WK  L  Y+D+M   GPPGAS NGFNEN
Sbjct: 187 WGENMALLTATANSYGARWFDEKWTPQFDQPEWKKALQFYVDLMKEAGPPGASSNGFNEN 246

Query: 248 LALFQQGKCGMWIDATVAASFVTNPEESTVADKVGFALAPDTGKGKRANWLGAWNLAIPA 307
           LALFQ GKCG+WIDATVAASFVTNP+ES VAD+VG+AL P  G     NWL AWNL +PA
Sbjct: 247 LALFQTGKCGIWIDATVAASFVTNPKESKVADQVGYALFPTGGVENHGNWLWAWNLGVPA 306

Query: 308 GSQKVDAAKQFIAWATSKDYAELVASKEGWANVPPGTRTSLYENPEYQK-VPFAKMTLDS 366
           G+QK +AA++F++WAT K Y+ELVASKEGWANVPPGTR SLY NPEY+K  PFAK+TLD+
Sbjct: 307 GTQKAEAAQKFVSWATDKAYSELVASKEGWANVPPGTRKSLYANPEYEKAAPFAKITLDA 366

Query: 367 INAADPTHPAVDPVPYVGVQFVAIPEFQGIGTAVGQQFSAALAGSMSAEQALQAAQQFTT 426
           +NAAD + P V PVPY G QFVAIPEFQGIGTAVGQQFSAALAGS+S +QALQ+AQQ TT
Sbjct: 367 MNAADTSKPTVKPVPYTGGQFVAIPEFQGIGTAVGQQFSAALAGSVSVDQALQSAQQLTT 426

Query: 427 REMTRAGYIK 436
           REMT+ GYIK
Sbjct: 427 REMTKGGYIK 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: 743
Number of extensions: 31
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 24 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