Alignments for a candidate for yveA in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for yveA in Cupriavidus basilensis 4G11

Align Aspartate-proton symporter; L-aspartate transporter (characterized)
to candidate RR42_RS36375 RR42_RS36375 aspartate:proton symporter

Query= SwissProt::O07002
         (520 letters)



>FitnessBrowser__Cup4G11:RR42_RS36375
          Length = 524

 Score =  671 bits (1731), Expect = 0.0
 Identities = 306/514 (59%), Positives = 411/514 (79%), Gaps = 1/514 (0%)

Query: 4   QGNFQKSMSLFDLILIGMGAIFGSAWLFAVSNVASKAGPSGAFSWILGGAIILLIGLVYA 63
           QG F++ +SL DL  IG+GAIFGS WLFA S+V++ AGP+G  SW+LGG  +LL+G+VY 
Sbjct: 5   QGKFKRQLSLTDLTFIGLGAIFGSGWLFAASHVSAIAGPAGIISWLLGGFAVLLLGIVYC 64

Query: 64  ELGAALPRTGGIIRYPVYSHGHLVGYLISFVTIVAYTSLISIEVTAVRQYVAYWFPGLTI 123
           ELGAALPR GGIIRYPV+SHG L+GYL+  +T++A++SLI+IEV A RQY A WFP L+ 
Sbjct: 65  ELGAALPRAGGIIRYPVFSHGELMGYLMGLITLIAFSSLIAIEVVAARQYAAAWFPFLSQ 124

Query: 124 KGSDSPTISGWILQFALLCLFFLLNYWSVKTFAKANFIISIFKYIVPITIIIVLIFHFQP 183
            GS +PT+ GW LQFA+LCLFF+LNY+SVKTFA+AN I+S+FK++VP+ +I+VL  HF+P
Sbjct: 125 PGSSNPTLPGWALQFAMLCLFFVLNYYSVKTFARANNIVSVFKFVVPLLVIVVLFTHFKP 184

Query: 184 ENLSVQGFAPFGFTGIQAAISTGGVMFAYLGLHPIVSVAGEVQNPKRNIPIALIICIIVS 243
            NL V GFAPFG +GIQAA+S GG++FAYLGL PI+SVA EV++P+R IPIALI+ +++S
Sbjct: 185 ANLQVHGFAPFGLSGIQAAVSAGGIIFAYLGLTPIISVASEVRSPQRTIPIALILSVLLS 244

Query: 244 TIIYTVLQVTFIGAIPTETLKHGWPAIGREFSLPFKDIAVMLGLGWLATLVILDAILSPG 303
           T+IY +LQ+ F+G +PTETL  GW  +G+ F+LP++DIA+ LG+GWLA LV+ DA++SP 
Sbjct: 245 TLIYVLLQIAFLGGVPTETLSDGWRGVGQAFALPYRDIALALGVGWLAFLVVSDAVISPS 304

Query: 304 GNGNIFMNTTSRLVYAWARNGTLFGIFSKVNKDTGTPRASLWLSFALSIFWTLPFPSWNA 363
           G GNI+MN T R+VY WAR GT F  FS+++  +G PR +LWL+FALS+FWTLPFPSW A
Sbjct: 305 GTGNIYMNATPRVVYGWARGGTFFKSFSRIDAASGIPRPALWLTFALSVFWTLPFPSWEA 364

Query: 364 LVNVCSVALILSYAIAPISSAALRVNAKDLNRPFYLKGMSIIGPLSFIFTAFIVYWSGWK 423
           ++NV S AL+LSYA+AP++ AALR NA  L+RPF ++ ++++GPLSFI  A IVYWSGW 
Sbjct: 365 MINVVSAALVLSYAVAPVTVAALRRNAPSLHRPFRVRWLAVLGPLSFIIAALIVYWSGWG 424

Query: 424 TVSWLLGSQLVMFLIYLCFSKYTPKEDVSLAQQLKSAWWLIGFYIMMLIFSYIGSFGHGL 483
           TVSWLLG Q+ MF++YL   +  P   +SLAQQ+KS+ WLI FY+++++ SY+G+FG G+
Sbjct: 425 TVSWLLGLQIAMFVVYLLCRRAVPTHRLSLAQQVKSSLWLIAFYLLIIVASYLGTFG-GI 483

Query: 484 GIISNPVDLILVAIGSLAIYYWAKYTGLPKAAID 517
           G IS+P D  LVA+ +L IY W   TG+P A +D
Sbjct: 484 GAISHPWDTGLVALIALGIYGWGARTGIPAALLD 517


Lambda     K      H
   0.328    0.143    0.451 

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: 1018
Number of extensions: 45
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: 520
Length of database: 524
Length adjustment: 35
Effective length of query: 485
Effective length of database: 489
Effective search space:   237165
Effective search space used:   237165
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 (21.7 bits)
S2: 52 (24.6 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
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