GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctA in Herbaspirillum seropedicae SmR1

Align Fumarate:H+ symporter of 442 aas and 14 established TMSs, DctA. Responsible for the transport of dicarboxylates such as succinate, fumarate, and malate (characterized)
to candidate HSERO_RS22690 HSERO_RS22690 C4-dicarboxylate ABC transporter

Query= TCDB::Q1J1H5
         (442 letters)



>FitnessBrowser__HerbieS:HSERO_RS22690
          Length = 444

 Score =  453 bits (1166), Expect = e-132
 Identities = 235/425 (55%), Positives = 310/425 (72%), Gaps = 3/425 (0%)

Query: 3   KIFRSLYVQVLIAIVLGILVGFLFPSFGEGLKPLGDGFIKLIKMLIAPIIFATVVSGIAH 62
           K+F+SL+ QV++A++ GI++G  +P FG+ LKPLGDGFIKLIKM+I  I+F  VV GI  
Sbjct: 3   KLFKSLFGQVVLALIGGIIIGLFWPDFGQNLKPLGDGFIKLIKMIIPVIVFCVVVQGICG 62

Query: 63  MRDTKKVGRVGGKALIYFEVVTTFALVIGLVVANILKPGHGMNVNPATLDTSAISKYTQA 122
             D KKVG VG KA+IYFEVVTT AL++GLV+A +++PG GMN++P+ LD S++S Y   
Sbjct: 63  ASDLKKVGSVGVKAIIYFEVVTTIALLLGLVLALVVQPGAGMNIDPSNLDASSLSGYMAN 122

Query: 123 AG---EQSVADFLLHIIPNTLVSAFTEGDLLQVLLISVLFGFALTQLGTLGQKVLAGIEA 179
           AG   E   A+F++ +IP T VSAFT GD+LQVLLISV FG AL  +G  G  V+A + +
Sbjct: 123 AGKVKETGFAEFIMKLIPATAVSAFTSGDVLQVLLISVTFGCALLLIGEKGAPVVALVAS 182

Query: 180 VNSAVFVILGFVMRLAPIGAFGAMAFTIGKYGVGTLAQLAYLMVAFYATCLLFVFVVLGL 239
           ++ A F  + F +RLAP+G  GA+AFT+GKYG+G+L QLA L++ FY   + FV VVLG 
Sbjct: 183 LSDAFFKCMSFFIRLAPLGVLGAIAFTVGKYGIGSLKQLALLVLLFYGAVIFFVLVVLGG 242

Query: 240 IARFAGFSILKFIRFIKEELLLVLGTSSSESALPRLITKLEYAGANRSVVGLVVPAGYSF 299
           I R +G SI K IR+++EEL++VL T+SS+S LP+++ KLE+ G  +S VGLV+P GYSF
Sbjct: 243 ILRASGLSIFKLIRYLREELVVVLATTSSDSVLPQIMKKLEHMGIKKSTVGLVIPTGYSF 302

Query: 300 NLDGTSIYLTMATLFIAQATNTHLSLGQQLGILGVLLLTSKGAAGVTGSGFITLAATLSA 359
           NLD  SIYLTMA LFIAQATNTHLS+G    IL + L+TSKGA GV GS  + LAATL+ 
Sbjct: 303 NLDAFSIYLTMAALFIAQATNTHLSMGDLAAILAIALVTSKGAHGVPGSAIVILAATLTT 362

Query: 360 VGHVPVAGLALILGIDRFMSEARALTNFVGNGVATLVIARSEKALDTNRLQRVLNGEVLP 419
           +  +PV GL L+L ID F+  ARAL N +GN VAT+VIA  E+ +D  R + VLNGE + 
Sbjct: 363 IPAIPVVGLVLVLSIDWFIGIARALGNLLGNCVATVVIASWERDIDKVRARAVLNGESVA 422

Query: 420 PATPE 424
           P   E
Sbjct: 423 PLVEE 427


Lambda     K      H
   0.325    0.142    0.398 

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: 551
Number of extensions: 28
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: 442
Length of database: 444
Length adjustment: 32
Effective length of query: 410
Effective length of database: 412
Effective search space:   168920
Effective search space used:   168920
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (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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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