Alignments for a candidate for araG in Pseudarthrobacter sulfonivorans Ar51

GapMind for catabolism of small carbon sources

Alignments for a candidate for araG in Pseudarthrobacter sulfonivorans Ar51

Align L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized)
to candidate WP_058930145.1 AU252_RS07280 sugar ABC transporter ATP-binding protein

Query= CharProtDB::CH_014279
         (504 letters)



>NCBI__GCF_001484605.1:WP_058930145.1
          Length = 506

 Score =  343 bits (881), Expect = 6e-99
 Identities = 190/497 (38%), Positives = 297/497 (59%), Gaps = 4/497 (0%)

Query: 3   QSTPYLSFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTG 62
           Q  P L  RG+ K F GV+AL  +      G+VH +MG+NGAGKSTL+K LSG + P  G
Sbjct: 6   QPRPLLEVRGLTKRFAGVQALKGVDLQVLPGEVHCVMGQNGAGKSTLIKTLSGVHQPDGG 65

Query: 63  SVVINGQEMSFSDTTAALNAGVAIIYQELHLVPEMTVAENIYLGQLPHKGGIVNRSLLNY 122
            +   G++++    TAAL+ G+A +YQEL +V  ++VAENI+LG     GG+++    N 
Sbjct: 66  EIRWEGKQITLPRPTAALDLGIATMYQELDVVDGLSVAENIFLGHERSTGGVLHVKKTNA 125

Query: 123 EAGLQLKHLGM-DIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDN 181
            A   LK LG   + P T +  LS    Q+V +A+AL+R+ K+I  DEP++ L + E+ N
Sbjct: 126 IARTLLKRLGHGSLSPSTEVGTLSAANKQIVSMARALSRDTKLIIMDEPSAILDSGEVSN 185

Query: 182 LFRVIRELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQAMV 241
           LFRV+REL  +G  ++Y+SHR+EEI  + D I+V KDGR       +       L++ M 
Sbjct: 186 LFRVVRELTAQGIAVVYISHRLEEIRQIGDRISVIKDGRSTANGLSVTDTQKSELIRLMT 245

Query: 242 GRDIGDIYGWQPRSYGEERLRLDA--VKAPGVRTPISLAVRSGEIVGLFGLVGAGRSELM 299
           GRD+ +++  +     +  + LD   ++  G    +SL VR+GEI+G  GLVG+ RSE++
Sbjct: 246 GRDVANVFPERKPVPADAPVVLDVDNLELYGHFEKVSLTVRAGEILGFAGLVGSKRSEIL 305

Query: 300 KGMFGGTQITAGQVYIDQQPIDIRKPSHAIAAGMMLCPEDRKAEGIIPVHSVRDNINISA 359
           + ++G  + ++G+V ++ + +     + A+ AG+ L PE+RK++G+I    +  N+ +S 
Sbjct: 306 ETIYGARKASSGRVSVNGKALRPGSVTSAVNAGIGLSPEERKSQGLILDEPLFKNVTLST 365

Query: 360 RRKHVLGGCVINNGWEENNADHHIRSLNIKTPGAEQLIMNLSGGNQQKAILGRWLSEEMK 419
             +    G  +N   E N A   I +L ++    ++    LSGGNQQK +L RWL     
Sbjct: 366 FERFARMG-YLNEAAERNAAREQIAALELRPADPDRPARTLSGGNQQKILLARWLVHGTS 424

Query: 420 VILLDEPTRGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRIVVMREGEIAG 479
           V+LLDEPTRG+DVGA+ EIY++I  LA  G A++  SS++ EVLG+AD ++V+ +G++  
Sbjct: 425 VLLLDEPTRGVDVGARSEIYDLIRKLAEAGTAIIVVSSEIEEVLGLADNVLVIDDGKVLT 484

Query: 480 ELLHEQADERQALSLAM 496
           +      DE   L L M
Sbjct: 485 QTKASDIDEHGVLDLVM 501



 Score = 87.0 bits (214), Expect = 1e-21
 Identities = 62/224 (27%), Positives = 109/224 (48%), Gaps = 8/224 (3%)

Query: 26  ISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGSVVINGQEMSFSDTTAALNAGVA 85
           +S    AG++    G  G+ +S +L+ + G    ++G V +NG+ +     T+A+NAG+ 
Sbjct: 281 VSLTVRAGEILGFAGLVGSKRSEILETIYGARKASSGRVSVNGKALRPGSVTSAVNAGIG 340

Query: 86  IIYQELH---LVPEMTVAENIYLGQLPH--KGGIVNRSLLNYEAGLQLKHLGM-DIDPDT 139
           +  +E     L+ +  + +N+ L       + G +N +     A  Q+  L +   DPD 
Sbjct: 341 LSPEERKSQGLILDEPLFKNVTLSTFERFARMGYLNEAAERNAAREQIAALELRPADPDR 400

Query: 140 PLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNLFRVIRELRKEGRVILYV 199
           P + LS G  Q + +A+ L     ++  DEPT  +       ++ +IR+L + G  I+ V
Sbjct: 401 PARTLSGGNQQKILLARWLVHGTSVLLLDEPTRGVDVGARSEIYDLIRKLAEAGTAIIVV 460

Query: 200 SHRMEEIFALSDAITVFKDGRYVKTFTDMQQVD-HDALVQAMVG 242
           S  +EE+  L+D + V  DG+ V T T    +D H  L   M G
Sbjct: 461 SSEIEEVLGLADNVLVIDDGK-VLTQTKASDIDEHGVLDLVMKG 503


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: 621
Number of extensions: 34
Number of successful extensions: 8
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: 506
Length adjustment: 34
Effective length of query: 470
Effective length of database: 472
Effective search space:   221840
Effective search space used:   221840
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 Apr 09 2024. 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