GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dauA in Cupriavidus basilensis 4G11

Align C4-dicarboxylic acid transporter DauA; Dicarboxylic acid uptake system A (characterized)
to candidate RR42_RS16025 RR42_RS16025 sulfate transporter

Query= SwissProt::P0AFR2
         (559 letters)



>FitnessBrowser__Cup4G11:RR42_RS16025
          Length = 596

 Score =  348 bits (893), Expect = e-100
 Identities = 217/581 (37%), Positives = 314/581 (54%), Gaps = 68/581 (11%)

Query: 24  YTAARFTRDLIAGITVGIIAIPLAMALAIGSGVAPQYGLYTAAVAGIVIALTGGSRFSVS 83
           Y  A F +DL AG+TVG++A+PLAMA AI SG+ PQ GL+TA +AG +IA  GGS   + 
Sbjct: 21  YNRALFFKDLAAGLTVGVVALPLAMAFAIASGMPPQAGLFTAIIAGFLIAALGGSPVQIG 80

Query: 84  GPTAAFVVILYPVSQQFGLAGLLVATLLSGIFLILMGLARFGRLIEYIPVSVTLGFTSGI 143
           GP  AF+VI+Y +  ++G+A LL+AT+L+G  L  MGL R G LI +IPV++ +GFT+GI
Sbjct: 81  GPAGAFIVIVYGIVARYGVANLLIATILAGGLLFAMGLFRLGTLIRFIPVAIVIGFTNGI 140

Query: 144 GITIGTMQIKDFLGLQMAHVPEHYLQKVGALFMALPTINVGDAAIGIVTLGILVFWPRLG 203
            + I   QI DFLGLQ   +P ++L ++  L  ALPT++    A+ + +L ++  W RL 
Sbjct: 141 AVLIMVSQIADFLGLQTGKLPGNFLSQMRVLGRALPTVSWPTVALAVSSLVVVAGWSRLA 200

Query: 204 I-------------------------------RLPGHLPALLAGCAVMGIVNLLGGHVAT 232
           +                                +PG + AL+   A  G+++L    V T
Sbjct: 201 LLAGKRWRPVSTVAANPANPPNAHGRLGRALAMVPGTVIALVLATAANGLLHL---PVET 257

Query: 233 IGSQFHYVLADGSQGNGIPQLLPQLVLPWDLPNSEFTLTWDSIRTLLPAAFSMAMLGAIE 292
           IG++F           GIPQ LP   LP         L+W  ++ L+    ++A+LGAIE
Sbjct: 258 IGTRF----------GGIPQGLPPFALP--------QLSWQLVQQLVAPTLTIALLGAIE 299

Query: 293 SLLCAVVLDGMTGTKHKANSELVGQGLGNIIAPFFGGITATAAIARSAANVRAGATSPIS 352
           SLLCA V D +   +H  N EL+ QG+ NI+ PFFGG+ AT  IAR+  NVR+G  +P++
Sbjct: 300 SLLCARVADSLIDDRHDPNQELMAQGIANIVTPFFGGLPATGTIARTVTNVRSGGRTPVA 359

Query: 353 AVIHSILVILALLVLAPLLSWLPLSAMAALLLMVAWNMSEAHKV-VDLLRHAPKDDIIVM 411
            +IH+  ++L +LV APL S +PL+ +AA+LL VAWNM E H   +  L+    +  I++
Sbjct: 360 GMIHAATLLLIVLVAAPLASAIPLATLAAILLYVAWNMGEWHMFGLTHLKRYSNNYRIIL 419

Query: 412 LLCMSLTVLFDMVIAISVGIVLASLLFMRRIARMTR---LAPVVVDVPDD--------VL 460
           L    LTV+FD+ +A+ VG+VLA L F+ R+A +T+   +AP  +    D        V 
Sbjct: 420 LGTFVLTVVFDLTVAVQVGLVLACLFFIYRMAALTQIEAIAPAALPPAADGRPLPAGEVA 479

Query: 461 VLRVIGPLFFAA---AEGLFTDLESRLEGKRIVILKWDAVPVLDAGGLDAFQRFVKRLP- 516
              + G LFF A    E L    +       ++IL    +  LD  GLD      K L  
Sbjct: 480 AYHMTGALFFGAVNKVEALIDPRDRTQPVPAVLILDVGKLVALDTTGLDTLDALRKTLAR 539

Query: 517 EGCELRVCNVEFQPLRTMARAGIQPIPGRLAFFPNRRAAMA 557
            G  L +C    Q +  M RAG     G   +     AA A
Sbjct: 540 RGGTLVICAAPAQVMSLMRRAGFLEQMGTANYCDTLAAACA 580


Lambda     K      H
   0.328    0.142    0.425 

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: 719
Number of extensions: 37
Number of successful extensions: 4
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: 559
Length of database: 596
Length adjustment: 36
Effective length of query: 523
Effective length of database: 560
Effective search space:   292880
Effective search space used:   292880
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: 53 (25.0 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