Aligments for a candidate for dauA in Magnetospirillum magneticum AMB-1

GapMind for catabolism of small carbon sources

Aligments for a candidate for dauA in Magnetospirillum magneticum AMB-1

Align C4-dicarboxylic acid transporter DauA; Dicarboxylic acid uptake system A (characterized)
to candidate WP_011386051.1 AMB_RS18695 sodium-independent anion transporter

Query= SwissProt::P0AFR2
         (559 letters)



>NCBI__GCF_000009985.1:WP_011386051.1
          Length = 569

 Score =  411 bits (1057), Expect = e-119
 Identities = 239/559 (42%), Positives = 335/559 (59%), Gaps = 43/559 (7%)

Query: 19  CWKEKYTAARFTRDLIAGITVGIIAIPLAMALAIGSGVAPQYGLYTAAVAGIVIALTGGS 78
           C KE Y   R   DLIAG+TV I+A+PLAMAL I SGV P  GL+TA VAG +I+  GGS
Sbjct: 23  CLKEGYDLPRGRGDLIAGLTVAIVALPLAMALGIASGVTPDRGLFTAIVAGFLISFLGGS 82

Query: 79  RFSVSGPTAAFVVILYPVSQQFGLAGLLVATLLSGIFLILMGLARFGRLIEYIPVSVTLG 138
           RF + GPT AFVV++Y + QQ G  GL++ATL++G+ L+L GLARFG +I+YIP  +  G
Sbjct: 83  RFQIGGPTGAFVVVVYNIVQQHGYDGLVLATLMAGVMLLLFGLARFGVVIKYIPYPLVTG 142

Query: 139 FTSGIGITIGTMQIKDFLGLQMAHVPEHYLQKVGALFMALPTINVGDAAIGIVTLGILVF 198
           FTSGI + I + Q+KDFLGL+M  VP  + +K  A    + T +    A+   TL +++ 
Sbjct: 143 FTSGIAVIIFSSQVKDFLGLRMESVPAEFFEKWVAYGEHIGTTHGPTLAVAAGTLAVILV 202

Query: 199 WPRLGIRLPGHLPALLAGCAVMGIVNLLGGHVATIGSQFHYVLADGSQGNGIPQLLPQLV 258
             R     PG L   + G +V  +V  LG  V TIGS+F           GIP  LP   
Sbjct: 203 LRRFRPGWPGFLIG-VTGASV--LVWALGMPVETIGSRF----------GGIPSTLPSPQ 249

Query: 259 LPWDLPNSEFTLTWDSIRTLLPAAFSMAMLGAIESLLCAVVLDGMTGTKHKANSELVGQG 318
            P         L+W  +  LL  AF++A L  IESLL A+V DGMTG +HK+N EL+ QG
Sbjct: 250 FP--------ALSWGKVTALLQPAFTIAFLAGIESLLSAMVADGMTGRRHKSNCELLAQG 301

Query: 319 LGNIIAPFFGGITATAAIARSAANVRAGATSPISAVIHSILVILALLVLAPLLSWLPLSA 378
           + NI +  FGGI AT AIAR+A ++++GA +P++ ++H++ ++L +L+ APL SW+PL +
Sbjct: 302 IANIASVLFGGIPATGAIARTATSIKSGAQTPVAGMLHAVFILLFMLLFAPLASWIPLPS 361

Query: 379 MAALLLMVAWNMSEAHKVVDLLRHAPKDDIIVMLLCMSLTVLFDMVIAISVGIVLASLLF 438
           +AA+L++VAWNMSEA   + L+  AP+ D  V+L+   LTV+ D+ +AI VG+VLAS+LF
Sbjct: 362 LAAVLMVVAWNMSEAPHFIHLM-SAPRSDRAVLLVTFVLTVMVDLTVAIEVGMVLASILF 420

Query: 439 MRRIARMTRL--------------------APVVVDVPDDVLVLRVIGPLFFAAAEGLFT 478
           MRR+A +T +                    A     +PD V V ++ GP FF  A  L  
Sbjct: 421 MRRMAEVTEIGTGIHLIDEDAEDGGDDHVGAIPTTPIPDGVEVFQISGPFFFGVATRLSE 480

Query: 479 DLESRLEGKRIVILKWDAVPVLDAGGLDAFQRFVKRL-PEGCELRVCNVEFQPLRTMARA 537
             E   +  R+ IL+   VPV+DA G+ A   FV+R    G E+ +  V+ QP++ M R 
Sbjct: 481 VFEQTHKPPRVFILRMRLVPVIDASGIQALTEFVRRCRKHGTEVLLSGVQPQPMQVMGRM 540

Query: 538 GIQPIPGRLAFFPNRRAAM 556
           G+    G   F PN  AA+
Sbjct: 541 GLCHEIGEDNFVPNIDAAL 559


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: 748
Number of extensions: 37
Number of successful extensions: 5
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: 569
Length adjustment: 36
Effective length of query: 523
Effective length of database: 533
Effective search space:   278759
Effective search space used:   278759
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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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, or view the source code.

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