Alignments for a candidate for araG in Pseudovibrio axinellae Ad2

GapMind for catabolism of small carbon sources

Alignments for a candidate for araG in Pseudovibrio axinellae Ad2

Align L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized)
to candidate WP_068005521.1 PsAD2_RS10155 ABC transporter ATP-binding protein

Query= CharProtDB::CH_014279
         (504 letters)



>NCBI__GCF_001623255.1:WP_068005521.1
          Length = 515

 Score =  262 bits (669), Expect = 2e-74
 Identities = 166/494 (33%), Positives = 267/494 (54%), Gaps = 12/494 (2%)

Query: 6   PYLSFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGSVV 65
           P LS + I K F  + A  +++ D +AG++ AL+GENGAGK+TL+ IL G+Y    G V+
Sbjct: 9   PLLSLQNITKIFGDLVANGNVNLDLHAGEIVALLGENGAGKTTLMNILFGHYVADEGRVM 68

Query: 66  INGQEMSFSDTT-----AALNAGVAIIYQELHLVPEMTVAENIYLGQLPHKGGIVNRSLL 120
           +     +  D       AAL AG+ +++Q   L   +T  ENI LG         +RS  
Sbjct: 69  VRTSSGTLVDLEPGAPQAALEAGIGMVHQHFTLAENLTGLENIVLGTESLFARKFSRSKA 128

Query: 121 NYEAGLQLKHLGMDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREID 180
             +    ++  G+++D D  +  L++G+ Q VEI KAL R+A+I+  DEPT+ L+ +E D
Sbjct: 129 RAKLQELMQSSGLEVDLDLRVSKLAVGERQRVEILKALYRDARILVLDEPTAVLTPQESD 188

Query: 181 NLFRVIRELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQAM 240
           +LF  ++ L  +G  I+++SH+M E+   SD + V + GR V       Q D   L + M
Sbjct: 189 SLFNTLKLLAAKGMAIIFISHKMAEVLGASDRVAVLRGGRIVADL-PTSQCDRHKLAELM 247

Query: 241 VGRDIGDIYGWQPRSYGEERLRLDAVKAPGVR---TPISLAVRSGEIVGLFGLVGAGRSE 297
           VG  +  +   +P + GEE L    V A   R     ++L++R GEI+GL G+ G G+S 
Sbjct: 248 VGHAV-QMAEREPGNPGEEILVFKGVSAGEGRELIENVNLSLRKGEIIGLAGVSGNGQSM 306

Query: 298 LMKGMFGGTQITAGQVYIDQQPIDIRKPSHAIAAGMMLCPEDRKAEGIIPVHSVRDNINI 357
           L K + G  + TAG V +  QP+     + AI +G+   PEDR  +GI+   SV +N+ +
Sbjct: 307 LAKVLSGLEEPTAGAVTLGSQPLKANAAA-AIQSGVARIPEDRHHDGIVGAMSVEENLVL 365

Query: 358 SARRKHVLGGC-VINNGWEENNADHHIRSLNIKTPGAEQLIMNLSGGNQQKAILGRWLSE 416
              RK       ++        A   I++ +I+  G   +   LSGGN QK +L R L +
Sbjct: 366 EEIRKPAYQRFGLLRFNEIRKRAQEAIKAYDIRCSGPLAVSRLLSGGNIQKIVLARTLDQ 425

Query: 417 EMKVILLDEPTRGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRIVVMREGE 476
           E  ++L  +P+RG+DVGA  +++  +     +G  VL  S DL E+  ++DRI V+  G 
Sbjct: 426 EPAIVLAAQPSRGLDVGATADVHRRLQEARDRGAGVLLISEDLDELFQLSDRIAVIHRGH 485

Query: 477 IAGELLHEQADERQ 490
           ++  +  E+ D++Q
Sbjct: 486 VSEPMASEELDKKQ 499



 Score = 78.6 bits (192), Expect = 5e-19
 Identities = 62/230 (26%), Positives = 112/230 (48%), Gaps = 22/230 (9%)

Query: 275 ISLAVRSGEIVGLFGLVGAGRSELMKGMFGGTQITAGQVYIDQQP---IDIRK--PSHAI 329
           ++L + +GEIV L G  GAG++ LM  +FG      G+V +       +D+    P  A+
Sbjct: 29  VNLDLHAGEIVALLGENGAGKTTLMNILFGHYVADEGRVMVRTSSGTLVDLEPGAPQAAL 88

Query: 330 AAGMMLCPEDRKAEGIIPVHSVRDNINISARRKHVLGG-CVINNGWEENNADHHIRSLNI 388
            AG+          G++  H      N++     VLG   +    +  + A   ++ L +
Sbjct: 89  EAGI----------GMVHQHFTLAE-NLTGLENIVLGTESLFARKFSRSKARAKLQEL-M 136

Query: 389 KTPGAEQ----LIMNLSGGNQQKAILGRWLSEEMKVILLDEPTRGIDVGAKHEIYNVIYA 444
           ++ G E      +  L+ G +Q+  + + L  + ++++LDEPT  +       ++N +  
Sbjct: 137 QSSGLEVDLDLRVSKLAVGERQRVEILKALYRDARILVLDEPTAVLTPQESDSLFNTLKL 196

Query: 445 LAAQGVAVLFASSDLPEVLGVADRIVVMREGEIAGELLHEQADERQALSL 494
           LAA+G+A++F S  + EVLG +DR+ V+R G I  +L   Q D  +   L
Sbjct: 197 LAAKGMAIIFISHKMAEVLGASDRVAVLRGGRIVADLPTSQCDRHKLAEL 246


Lambda     K      H
   0.319    0.136    0.391 

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: 606
Number of extensions: 36
Number of successful extensions: 10
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 504
Length of database: 515
Length adjustment: 34
Effective length of query: 470
Effective length of database: 481
Effective search space:   226070
Effective search space used:   226070
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 24 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:

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 2024 update 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