Alignments for a candidate for dauA in Halomonas desiderata SP1

GapMind for catabolism of small carbon sources

Alignments for a candidate for dauA in Halomonas desiderata SP1

Align C4-dicarboxylic acid transporter DauA; Dicarboxylic acid uptake system A (characterized)
to candidate WP_086510106.1 BZY95_RS11745 C4-dicarboxylic acid transporter DauA

Query= SwissProt::P0AFR2
         (559 letters)



>NCBI__GCF_002151265.1:WP_086510106.1
          Length = 581

 Score =  478 bits (1230), Expect = e-139
 Identities = 263/549 (47%), Positives = 364/549 (66%), Gaps = 13/549 (2%)

Query: 10  MPFRALIDACWKEKYTAARFTRDLIAGITVGIIAIPLAMALAIGSGVAPQYGLYTAAVAG 69
           +P  AL+ A W+E Y  A   RDL+AG+T+GI+A+PL+MALAI +GV PQ+GLYTA VAG
Sbjct: 14  LPGSALL-AAWREGYGLAELKRDLLAGLTIGIVAVPLSMALAIATGVPPQHGLYTAIVAG 72

Query: 70  IVIALTGGSRFSVSGPTAAFVVILYPVSQQFGLAGLLVATLLSGIFLILMGLARFGRLIE 129
            +IALTGGSRF++SGPTAAFVVIL+P+    GL GLL+ATL++G+ L+ +GLAR G LI+
Sbjct: 73  AIIALTGGSRFNISGPTAAFVVILFPIVASHGLGGLLIATLMAGLILVALGLARLGNLIQ 132

Query: 130 YIPVSVTLGFTSGIGITIGTMQIKDFLGLQMAHVPEHYLQKVGALFMALPTINVGDAAIG 189
           ++P  V LGFT+GI + I  +Q+ DFLGL    + +  L  +  +  ALP++   +  IG
Sbjct: 133 FVPYPVVLGFTAGIAVVIALLQLPDFLGLDDVALGDSTLHNLVTILHALPSLAPAELGIG 192

Query: 190 IVTLGILVFWPRLGIRLPGHLPALLAGCAVMGIVNLLGGHVATIGSQFHYVLADGSQGNG 249
           ++TLG L+ WPR  + +P  L  L  G          G  V TI S+F +    G  G+G
Sbjct: 193 LITLGTLILWPRSKLPVPAPLVGLAVGTLAALAATWWGMEVETIASRFSWEY-QGQSGSG 251

Query: 250 IPQLLPQLVLPWDLPNSE---FTLTWDSIRTLLPAAFSMAMLGAIESLLCAVVLDGMTGT 306
           IP   P LVLPW LP  +    T+ +  IR LL  A ++AML AIESLLCAVV DG+T T
Sbjct: 252 IPPFAPGLVLPWRLPGPDGLPLTVDFALIRELLGPALAIAMLAAIESLLCAVVADGLTRT 311

Query: 307 KHKANSELVGQGLGNIIAPFFGGITATAAIARSAANVRAGATSPISAVIHSILVILALLV 366
           +H  N+EL+GQGLGNI APFFGGITATAA+AR+A NVR+GA SP++AVIH+++V+LA++ 
Sbjct: 312 RHDPNAELIGQGLGNIAAPFFGGITATAALARTATNVRSGAFSPLAAVIHALVVLLAVVA 371

Query: 367 LAPLLSWLPLSAMAALLLMVAWNMSEAHKVVDLLRHAPKDDIIVMLLCMSLTVLFDMVIA 426
           LA +L+ +P++A+AALL ++AWNMSEA   +  L+ AP  D+ ++++C  LTV+FDMV+A
Sbjct: 372 LAGVLALVPMAALAALLFIIAWNMSEARHFMHTLKSAPGSDVAILVICFLLTVVFDMVLA 431

Query: 427 ISVGIVLASLLFMRRIARMT---RLAP----VVVDVPDDVLVLRVIGPLFFAAAEGLFTD 479
           ++VGI LA+ LF+RR+A +T   RL P       D+P  V +  + GPLFF AAE   + 
Sbjct: 432 VAVGIGLAAALFIRRMAHLTHARRLEPGHDEESRDLPRQVALYDINGPLFFGAAEKAVSS 491

Query: 480 LESRLEGKRIVILKWDAVPVLDAGGLDAFQRFVKRL-PEGCELRVCNVEFQPLRTMARAG 538
           L       R+V+L    VP LDA  + A Q  V+ L      L    +  + +  + RAG
Sbjct: 492 LRVVDPEVRVVMLDMRDVPSLDATAIVALQSLVEELSARQVGLIFIGMPARMVLKLKRAG 551

Query: 539 IQPIPGRLA 547
           ++   GRLA
Sbjct: 552 VKRQAGRLA 560


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: 793
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: 581
Length adjustment: 36
Effective length of query: 523
Effective length of database: 545
Effective search space:   285035
Effective search space used:   285035
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 24 2021. The underlying query database was built on Sep 17 2021.

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Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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