GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ackA in Herbaspirillum seropedicae SmR1

Align Acetate kinase; EC 2.7.2.1; Acetokinase (uncharacterized)
to candidate HSERO_RS01305 HSERO_RS01305 acetate kinase

Query= curated2:Q1QPW6
         (404 letters)



>FitnessBrowser__HerbieS:HSERO_RS01305
          Length = 397

 Score =  311 bits (798), Expect = 2e-89
 Identities = 182/402 (45%), Positives = 247/402 (61%), Gaps = 19/402 (4%)

Query: 4   ILVVNAGSSSVKFQVFSAEGEGKLLRQIKGQVDGIGSRP---RLRASGADNEPLADRAYP 60
           +L  NAGSS++K  VF  +G  +  +  +GQ+D +   P   RL   G  +E        
Sbjct: 5   LLTFNAGSSTIKLGVFRLDG-ARARKIGQGQLD-LHLAPLKLRLEIDGERSE-------- 54

Query: 61  IESVSDVPAAMGVAGGWLRDELRISPM-----AVGHRVVHGGPDYDRPVLIDHGVVARLE 115
           +E  +D  AAM      +  +L +        AVGHRVVHGG    + V +D  +   LE
Sbjct: 55  VEIDADPAAAMDRVLEQVLHQLEVGHAQGELCAVGHRVVHGGLHLAQAVRLDDAIETELE 114

Query: 116 RFVALAPLHQPNNLDPIRSLLANFPALPQVACFDTAFHRTHDAVADYYAIPYQFYVEGVR 175
               LAPLHQP NL  IR++    P LPQ A FDTAFH + DA+A  +A+P + + EGV 
Sbjct: 115 NLAPLAPLHQPQNLRLIRAIARLRPGLPQTASFDTAFHASQDALARRFALPRRLHEEGVL 174

Query: 176 RYGFHGLSYEYVAKTLPHVAPEIAKGRVIVAHLGSGASMCALKGGRSIESTMGFTALDGL 235
           RYGFHG+SY YVA  +   A   A  RV+VAHLG+GAS+CAL  GRS++++ GF+ LDG+
Sbjct: 175 RYGFHGISYSYVAAEMRRQALPEAHARVVVAHLGNGASLCALHAGRSVDASTGFSTLDGV 234

Query: 236 PMGTRPGQIDPGVVLYLVSEKGMSPAKAQDFLYRDCGLKGLSGVSNDMRELEASEDPKAK 295
           PMGTR G +D GV+LYL+  +GMS  + +D LY   GL G+SG+S D+R L+ S+D  A+
Sbjct: 235 PMGTRCGALDAGVLLYLL-RQGMSLDELEDLLYHRSGLLGVSGLSADVRSLQQSQDSAAR 293

Query: 296 LAVDYFVYRVGLNAGMLAAALQGLDAFVFTAGIGENSMRIRARIADQLAWLGVTLDPTQN 355
            A+D F  R    A  LA+ L G+DA VFTAGIGE+   +RA I ++L WLGV LDP  N
Sbjct: 294 EALDLFALRCAGEAARLASTLGGIDALVFTAGIGEHDAAMRAAICERLGWLGVRLDPQAN 353

Query: 356 SRHARLISGSDSRIPVYVIPTDEELMIAQHTLSLLLDRSSSS 397
           + HA  IS +DS + VYVIPT+EE +IA    +LLL  ++ +
Sbjct: 354 AAHAGRISRADSAVSVYVIPTNEEQVIADDAAALLLTSATGT 395


Lambda     K      H
   0.320    0.137    0.403 

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: 441
Number of extensions: 16
Number of successful extensions: 2
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: 404
Length of database: 397
Length adjustment: 31
Effective length of query: 373
Effective length of database: 366
Effective search space:   136518
Effective search space used:   136518
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: 50 (23.9 bits)

Align candidate HSERO_RS01305 HSERO_RS01305 (acetate kinase)
to HMM TIGR00016 (ackA: acetate kinase (EC 2.7.2.1))

Software error:

../bin/blast/fastacmd -i /tmp/list.2029.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.2029.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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