GapMind for catabolism of small carbon sources

 

Alignments for a candidate for chvE in Acidovorax sp. GW101-3H11

Align CVE1 aka ChvE aka ATU2348 aka AGR_C_4267, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate Ac3H11_610 L-arabinose-binding periplasmic protein precursor AraF (TC 3.A.1.2.2)

Query= TCDB::P25548
         (354 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_610
          Length = 356

 Score =  541 bits (1395), Expect = e-159
 Identities = 272/353 (77%), Positives = 306/353 (86%), Gaps = 3/353 (0%)

Query: 2   KSIISLMAACAIGAASFAAPAFAQDKGSVGIAMPTKSSARWIDDGNNIVKQLQEAGYKTD 61
           K++++ MA  AIGA S A+   AQDKG++GI+MPTKSSARWI DG+N+VK L+E GYKTD
Sbjct: 7   KAVLASMALTAIGATSVAS---AQDKGAIGISMPTKSSARWIADGDNMVKVLKERGYKTD 63

Query: 62  LQYADDDIPNQLSQIENMVTKGVKVLVIASIDGTTLSDVLKQAGEQGIKVIAYDRLIRNS 121
           LQYADDDIPNQL+QIENM+TKG KVLVIASIDGTTLS  L+ A ++G+KVIAYDRLI+ S
Sbjct: 64  LQYADDDIPNQLAQIENMITKGAKVLVIASIDGTTLSKALQNAADKGVKVIAYDRLIKGS 123

Query: 122 GDVSYYATFDNFQVGVLQATSITDKLGLKDGKGPFNIELFGGSPDDNNAFFFYDGAMSVL 181
            +V YYATFDNFQVGVLQATSI DKLGLK GKGPFNIELFGGSPDDNNAFFFYDGAMSVL
Sbjct: 124 KNVDYYATFDNFQVGVLQATSIVDKLGLKQGKGPFNIELFGGSPDDNNAFFFYDGAMSVL 183

Query: 182 KPYIDSGKLVVKSGQMGMDKVGTLRWDPATAQARMDNLLSAYYTDAKVDAVLSPYDGLSI 241
           +PYIDSGKLVV+S Q GM+KVGTLRWD + AQARMDNLLSAYY   KV AVLSPYDG+SI
Sbjct: 184 QPYIDSGKLVVRSKQTGMNKVGTLRWDGSVAQARMDNLLSAYYGKDKVHAVLSPYDGISI 243

Query: 242 GIISSLKGVGYGTKDQPLPVVSGQDAEVPSVKSIIAGEQYSTIFKDTRELAKVTVNMVNA 301
           GI+SSLKGVGY T  QP PVVSGQDAEVPS+KSI+ GEQ ST+FKDTRELAKV  NMV+A
Sbjct: 244 GILSSLKGVGYCTAQQPCPVVSGQDAEVPSIKSILKGEQSSTVFKDTRELAKVAANMVDA 303

Query: 302 VMEGKEPEVNDTKTYENGVKVVPSYLLKPVAVTKENYKQVLVDGGYYKEDQLK 354
           V+ GK+PE+NDTKTY NGVKVVPSYLLKPVAV   N+  VLV  GYYKE Q+K
Sbjct: 304 VLTGKQPEINDTKTYNNGVKVVPSYLLKPVAVDSSNWNAVLVGSGYYKESQIK 356


Lambda     K      H
   0.314    0.133    0.372 

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: 549
Number of extensions: 20
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: 354
Length of database: 356
Length adjustment: 29
Effective length of query: 325
Effective length of database: 327
Effective search space:   106275
Effective search space used:   106275
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 49 (23.5 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:

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