GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aacS in Paraburkholderia bryophila 376MFSha3.1

Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate H281DRAFT_04125 H281DRAFT_04125 Acyl-CoA synthetase (AMP-forming)/AMP-acid ligase II

Query= reanno::acidovorax_3H11:Ac3H11_3009
         (578 letters)



>FitnessBrowser__Burk376:H281DRAFT_04125
          Length = 520

 Score =  217 bits (552), Expect = 1e-60
 Identities = 178/563 (31%), Positives = 267/563 (47%), Gaps = 63/563 (11%)

Query: 16  SHARGATDVPLIEQTIGAFFADMVA----RQPEREALVSVHQGRRYTYAQLQTEAHRLAS 71
           S  R   DVP +   + A  +D+ A    R P+  AL+    GRR T AQL       A+
Sbjct: 5   SPLRSRIDVPALLAALPARISDIPALAAGRDPQHVALIE--DGRRLTNAQLVQAVEATAA 62

Query: 72  ALLGMGLTPGDRVGIWSHNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKL 131
            L   G+  GDRV I + N+   +++  ATA                       ++    
Sbjct: 63  LLRDWGVRGGDRVMIVAENSIAQIVLLFATA-----------------------RLDAWA 99

Query: 132 LVSMARFKTSDYLGMLRELAPEWQGQQPGHLQAAKLPQLKT-VVWIDDEAGQGADEPGLL 190
           LVS AR   S+ L  +R            H Q    P++   VV    +AGQ A   G  
Sbjct: 100 LVSNARLSASE-LDAIR-----------AHAQ----PRVTAYVVESSADAGQHAQRHGAS 143

Query: 191 RFTELIARGNAADPRLAQVAAGLQATDPIN------IQFTSGTTGFPKGATLTHRNILNN 244
              + +A G  A        A  +  +  N      + +T+GTTG PKG  L+HRN+L  
Sbjct: 144 AAPD-VAPGIGAWSFTVDTFAQAEPVEAANDRQCAALIYTTGTTGAPKGVMLSHRNLLFI 202

Query: 245 GFFIGECMKLTPADRLCIPVPLYHCFGMVLGNLACFTHGATI-VYPNDGFDPLTVLQTVQ 303
                   ++ P D +   +P+ H +G     L     GAT+ + P   F P  V + + 
Sbjct: 203 AAVSSRLRQVRPDDVVYAVLPISHVYGFASVCLGSLYAGATLRLAPR--FAPGAVRRALA 260

Query: 304 DERCTGLHGVPTMFIAELDHPRFA--EFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREI 361
           DER +   GVP M    ++H +     ++   LR     GSP     +K  VE +    +
Sbjct: 261 DERVSIFQGVPAMHAKLIEHLQTHGHAWHAPHLRFIYSGGSPLDA-ALKAHVESVYGLPL 319

Query: 362 TIAYGMTETSPVSCQSSTDTPLSKRVSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTK 421
              YGMTE+SP   Q+  D P  +R  +VG+V P +EV+ V  D GA V +G+ GE   +
Sbjct: 320 HNGYGMTESSPTVSQTMLDAP--RRDCSVGEVIPGVEVRFVGLD-GADVAVGETGELWVR 376

Query: 422 GYSVMHGYWGDEAKTREAIDEGGWMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPRE 481
           G +VM GY+ +  +TR A+ + GW+ TGDLA  DA+G ++IVGR KD++IR G N+YP E
Sbjct: 377 GPNVMLGYYRNPQQTRAAVTQDGWLKTGDLARQDADGALHIVGRSKDLIIRSGFNVYPAE 436

Query: 482 IEEFLYRHPQVQDVQVVGVPDQKYGEELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPR 541
           +E  L  HPQV    V+G P +   EE+ A++        T  ++ A+C  ++A YK P 
Sbjct: 437 VEHVLNAHPQVVQSAVIGRPVEG-NEEVIAFVELAANASVTPAELTAWCVERLAPYKRPA 495

Query: 542 YIRFVTSFPMTVTGKIQKFKIRD 564
            ++ + + P   TGKI K ++R+
Sbjct: 496 EVKVLAALPAASTGKILKHRLRE 518


Lambda     K      H
   0.320    0.136    0.412 

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: 652
Number of extensions: 33
Number of successful extensions: 7
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: 578
Length of database: 520
Length adjustment: 36
Effective length of query: 542
Effective length of database: 484
Effective search space:   262328
Effective search space used:   262328
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 (21.8 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