GapMind for catabolism of small carbon sources

 

Alignments 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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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