GapMind for catabolism of small carbon sources

 

Aligments for a candidate for araG in Pseudomonas fluorescens FW300-N1B4

Align L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized)
to candidate Pf1N1B4_410 L-arabinose transport ATP-binding protein AraG (TC 3.A.1.2.2)

Query= CharProtDB::CH_014279
         (504 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_410 L-arabinose transport
           ATP-binding protein AraG (TC 3.A.1.2.2)
          Length = 514

 Score =  571 bits (1472), Expect = e-167
 Identities = 290/491 (59%), Positives = 367/491 (74%)

Query: 8   LSFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGSVVIN 67
           L F GIGKTFPGVKAL  ISF  + GQVHALMGENGAGKSTLLKIL G Y P++G + I 
Sbjct: 16  LRFNGIGKTFPGVKALDGISFVAHPGQVHALMGENGAGKSTLLKILGGAYTPSSGDLQIG 75

Query: 68  GQEMSFSDTTAALNAGVAIIYQELHLVPEMTVAENIYLGQLPHKGGIVNRSLLNYEAGLQ 127
            Q+  F  T  ++ +GVA+I+QELHLVPEMTVAEN++LG LP   G++NR +L  +A   
Sbjct: 76  EQKRIFKSTADSIGSGVAVIHQELHLVPEMTVAENLFLGHLPASFGLINRGVLRQQALAC 135

Query: 128 LKHLGMDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNLFRVIR 187
           LK L  +IDP   +  LS+GQ Q+VEIAKAL+R A +IAFDEPTSSLSAREID L  +I 
Sbjct: 136 LKGLADEIDPQEKVGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLMAIIG 195

Query: 188 ELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQAMVGRDIGD 247
            LR EG+V+LYVSHRMEE+F + +A+TVFKDGR+V+TF DM  + HD LV  MVGRDI D
Sbjct: 196 RLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRFVRTFEDMSALTHDQLVTCMVGRDIQD 255

Query: 248 IYGWQPRSYGEERLRLDAVKAPGVRTPISLAVRSGEIVGLFGLVGAGRSELMKGMFGGTQ 307
           IY ++ R  G   L++D +  PG+R P+S     GEI+GLFGLVGAGR+EL + + G T+
Sbjct: 256 IYDYRSRPRGAVALKVDGLLGPGLREPVSFEAHKGEILGLFGLVGAGRTELFRMLSGLTR 315

Query: 308 ITAGQVYIDQQPIDIRKPSHAIAAGMMLCPEDRKAEGIIPVHSVRDNINISARRKHVLGG 367
            TAG++ +  + + +  P  AIAAG++LCPEDRK EGI+P+ SV +NINISAR  H   G
Sbjct: 316 NTAGRLELRGRELKLHSPRDAIAAGILLCPEDRKKEGILPLASVAENINISARGAHSTFG 375

Query: 368 CVINNGWEENNADHHIRSLNIKTPGAEQLIMNLSGGNQQKAILGRWLSEEMKVILLDEPT 427
           C++   WE++NAD  I++L +KTP A Q IM LSGGNQQKAILGRWLS  MKV+LLDEPT
Sbjct: 376 CLLRGLWEKDNADKQIKALKVKTPNAAQKIMYLSGGNQQKAILGRWLSMPMKVLLLDEPT 435

Query: 428 RGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRIVVMREGEIAGELLHEQAD 487
           RGID+GAK EIY +I+ LAA G+AV+  SSDL EV+G++DRI+V+ EG + GEL  EQA+
Sbjct: 436 RGIDIGAKAEIYQIIHNLAASGIAVIVVSSDLMEVMGISDRILVLCEGAMRGELTREQAN 495

Query: 488 ERQALSLAMPK 498
           E   L LA+P+
Sbjct: 496 ESNLLQLALPR 506



 Score = 79.0 bits (193), Expect = 4e-19
 Identities = 63/239 (26%), Positives = 114/239 (47%), Gaps = 11/239 (4%)

Query: 18  PGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGSVVINGQEMSFSDTT 77
           PG++    +SF+ + G++  L G  GAG++ L ++LSG    T G + + G+E+      
Sbjct: 277 PGLRE--PVSFEAHKGEILGLFGLVGAGRTELFRMLSGLTRNTAGRLELRGRELKLHSPR 334

Query: 78  AALNAGVAIIYQELH---LVPEMTVAENIYLGQLPHKG--GIVNRSLLNYE-AGLQLKHL 131
            A+ AG+ +  ++     ++P  +VAENI +         G + R L   + A  Q+K L
Sbjct: 335 DAIAAGILLCPEDRKKEGILPLASVAENINISARGAHSTFGCLLRGLWEKDNADKQIKAL 394

Query: 132 GMDIDPDTPLK--YLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNLFRVIREL 189
            +   P+   K  YLS G  Q   + + L+   K++  DEPT  +       ++++I  L
Sbjct: 395 KVKT-PNAAQKIMYLSGGNQQKAILGRWLSMPMKVLLLDEPTRGIDIGAKAEIYQIIHNL 453

Query: 190 RKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQAMVGRDIGDI 248
              G  ++ VS  + E+  +SD I V  +G      T  Q  + + L  A+  + + D+
Sbjct: 454 AASGIAVIVVSSDLMEVMGISDRILVLCEGAMRGELTREQANESNLLQLALPRQRVADV 512


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: 750
Number of extensions: 35
Number of successful extensions: 5
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: 514
Length adjustment: 34
Effective length of query: 470
Effective length of database: 480
Effective search space:   225600
Effective search space used:   225600
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 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, 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