Alignments for a candidate for araG in Rhodobacter viridis JA737

GapMind for catabolism of small carbon sources

Alignments for a candidate for araG in Rhodobacter viridis JA737

Align L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized)
to candidate WP_110805879.1 C8J30_RS10885 sugar ABC transporter ATP-binding protein

Query= CharProtDB::CH_014279
         (504 letters)



>NCBI__GCF_003217355.1:WP_110805879.1
          Length = 511

 Score =  365 bits (936), Expect = e-105
 Identities = 205/479 (42%), Positives = 305/479 (63%), Gaps = 8/479 (1%)

Query: 8   LSFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGSVVIN 67
           LS RG  K +PG +AL  + FD   G V+ L+GENGAGKSTL+K+++G    T G++ ++
Sbjct: 9   LSIRGGVKVYPGTRALKGVDFDLRMGAVNVLVGENGAGKSTLMKLIAGVEDMTEGTITMD 68

Query: 68  GQEMSFSDTTAALNAGVAIIYQELHLVPEMTVAENIYLGQLPHKGGIVNRSLLNYEAGLQ 127
           G+EM F     A+ AG+ I++QEL+L P ++VAENI++G    +GGI      + EA  Q
Sbjct: 69  GREMRFRTKADAVAAGIGIVFQELNLFPNLSVAENIFIGHETTRGGIDIDIEAHREATRQ 128

Query: 128 L-KHLGMDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNLFRVI 186
           L + L  +I PDTPL  L IGQ Q+VEIAKALA+NA+I+  DEPTS+LSA E++ LFRVI
Sbjct: 129 LMERLEQNIHPDTPLGNLRIGQQQIVEIAKALAQNARILILDEPTSALSAAEVEVLFRVI 188

Query: 187 RELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQAMVGRDIG 246
            EL  +G  I+Y+SHR+EE+  + D ITV +DG  +     M+ VD   +V+AM+G    
Sbjct: 189 DELTAQGVGIVYISHRLEELIRVGDYITVLRDG-VITGARSMEGVDIPWIVKAMIGSSSK 247

Query: 247 DIYGWQPRSYGEERLRLDAVKAPGVR-----TPISLAVRSGEIVGLFGLVGAGRSELMKG 301
           +    +  ++G E  R + +  P          +SL++RSGEIVGL+GL+GAGRSE ++ 
Sbjct: 248 EYGRSEVANFGPEIFRAEDITLPRAGGGFTVDHVSLSIRSGEIVGLYGLMGAGRSEFLEC 307

Query: 302 MFGGTQITAGQVYIDQQPIDIRKPSHAIAAGMMLCPEDRKAEGIIPVHSVRDNINISARR 361
           +      + G+ +++ +P+  R     IA G+ L PEDRK +G+I + S+R+N+ +S+  
Sbjct: 308 VMAQHPHSGGKFWVEGKPLTERDVPGRIARGIALIPEDRKRDGLIQIMSIRENLTLSSLP 367

Query: 362 KHVLGGCVINNGWEENNADHHIRSLNIKTPGAEQLIMNLSGGNQQKAILGRWLSEEMKVI 421
                   ++   E   A   I+ L IK    E  + +LSGGNQQK ++G+ L    KV+
Sbjct: 368 SFTKL-FHLDLKKEAKTAVEFIKRLTIKVASPENPVSSLSGGNQQKVVIGKALMTGPKVL 426

Query: 422 LLDEPTRGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRIVVMREGEIAGE 480
           L+DEP+RGID+GAK E++  +  LAA+G+ +LF +SDL EVL ++DRI+VM +G + GE
Sbjct: 427 LMDEPSRGIDIGAKAEVFRTMRRLAAEGLGILFVTSDLDEVLALSDRIIVMAQGRVTGE 485



 Score = 88.2 bits (217), Expect = 6e-22
 Identities = 65/225 (28%), Positives = 106/225 (47%), Gaps = 9/225 (4%)

Query: 10  FRGIGKTFP---GVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGSVVI 66
           FR    T P   G   +  +S    +G++  L G  GAG+S  L+ +   +  + G   +
Sbjct: 262 FRAEDITLPRAGGGFTVDHVSLSIRSGEIVGLYGLMGAGRSEFLECVMAQHPHSGGKFWV 321

Query: 67  NGQEMSFSDTTAALNAGVAIIYQELH---LVPEMTVAENIYLGQLPHKGGIVNRSLLNYE 123
            G+ ++  D    +  G+A+I ++     L+  M++ EN+ L  LP    + +  L    
Sbjct: 322 EGKPLTERDVPGRIARGIALIPEDRKRDGLIQIMSIRENLTLSSLPSFTKLFHLDLKKEA 381

Query: 124 --AGLQLKHLGMDI-DPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREID 180
             A   +K L + +  P+ P+  LS G  Q V I KAL    K++  DEP+  +      
Sbjct: 382 KTAVEFIKRLTIKVASPENPVSSLSGGNQQKVVIGKALMTGPKVLLMDEPSRGIDIGAKA 441

Query: 181 NLFRVIRELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTF 225
            +FR +R L  EG  IL+V+  ++E+ ALSD I V   GR    F
Sbjct: 442 EVFRTMRRLAAEGLGILFVTSDLDEVLALSDRIIVMAQGRVTGEF 486



 Score = 82.0 bits (201), Expect = 5e-20
 Identities = 64/221 (28%), Positives = 106/221 (47%), Gaps = 8/221 (3%)

Query: 269 PGVRT--PISLAVRSGEIVGLFGLVGAGRSELMKGMFGGTQITAGQVYIDQQPIDIRKPS 326
           PG R    +   +R G +  L G  GAG+S LMK + G   +T G + +D + +  R  +
Sbjct: 19  PGTRALKGVDFDLRMGAVNVLVGENGAGKSTLMKLIAGVEDMTEGTITMDGREMRFRTKA 78

Query: 327 HAIAAGMMLCPEDRKAEGIIPVHSVRDNINISARRKHVLGGCVINNGWEENNADHHIRSL 386
            A+AAG+ +  ++     + P  SV +NI I    +   GG  I+       A   +   
Sbjct: 79  DAVAAGIGIVFQELN---LFPNLSVAENIFIG--HETTRGGIDIDIE-AHREATRQLMER 132

Query: 387 NIKTPGAEQLIMNLSGGNQQKAILGRWLSEEMKVILLDEPTRGIDVGAKHEIYNVIYALA 446
             +    +  + NL  G QQ   + + L++  ++++LDEPT  +       ++ VI  L 
Sbjct: 133 LEQNIHPDTPLGNLRIGQQQIVEIAKALAQNARILILDEPTSALSAAEVEVLFRVIDELT 192

Query: 447 AQGVAVLFASSDLPEVLGVADRIVVMREGEIAGELLHEQAD 487
           AQGV +++ S  L E++ V D I V+R+G I G    E  D
Sbjct: 193 AQGVGIVYISHRLEELIRVGDYITVLRDGVITGARSMEGVD 233


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: 656
Number of extensions: 34
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 504
Length of database: 511
Length adjustment: 34
Effective length of query: 470
Effective length of database: 477
Effective search space:   224190
Effective search space used:   224190
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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Candidates (tab-delimited)
Steps (tab-delimited)
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 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