GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bztC in Dinoroseobacter shibae DFL-12

Align BztC, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate 3606890 Dshi_0320 polar amino acid ABC transporter, inner membrane subunit (RefSeq)

Query= TCDB::Q52665
         (434 letters)



>FitnessBrowser__Dino:3606890
          Length = 432

 Score =  455 bits (1170), Expect = e-132
 Identities = 230/440 (52%), Positives = 302/440 (68%), Gaps = 14/440 (3%)

Query: 1   MSDT----SFVRTEMLAPRPAPVSQVGAIKWMRENLFSGPLNTALTVFGLLATVWLVQAA 56
           MSDT    +FVRTE + P P PVS+VG + W+R NLF    ++ LT+       WL    
Sbjct: 1   MSDTHASAAFVRTEEIPPSPPPVSEVGIVNWLRSNLFYSIPSSILTLLTAAFIYWLSSIL 60

Query: 57  APWLLHGVWNANSLTECRAIIAERWGPEATGACWAVIRVRWNQFLFGFYPVDQYWRLFVT 116
            PW+ +GVW+ANS+ +CR I+       A G C+AVI  RW Q +FG YP ++YWR  + 
Sbjct: 61  MPWMFNGVWDANSIRDCREIL-----DGAIGGCFAVIAERWPQLIFGNYPNEEYWRAVLA 115

Query: 117 FAGLFLALAPVLFDALPRKLIWGTLLYPLAAFWLLWGGPIWGPVSVLAGFAILGLLFTAL 176
           F GLF+ALAPVLF  LPRK++W T L+P  A+WL+WGG  W  V  L G  +  + F AL
Sbjct: 116 FVGLFVALAPVLFFKLPRKMLWFTGLFPFIAYWLIWGGSAWVSVMALVGVVVGYVAFKAL 175

Query: 177 APK--LGVPVSAGIGLVVAALFWLYAAAPIEAALQSALPLALPEVDSDQFGGFLLALVIG 234
             +   G  V+A   L    LFW++ +     AL S + L+LP+V+S   GGF++  ++G
Sbjct: 176 EERSFFGAIVAA---LFATLLFWIFISPLAVNALSSVVALSLPQVESRFIGGFMINFILG 232

Query: 235 VTAIVVSLPLGILLALGRQSDMLIVKSLSVGIIEFVRGVPLITLLFTASLLLQYFLPPGT 294
            + I +SLPLGI LALGRQS++ I+K + V  IEF+RGVPLITLLF AS++L YFLPPGT
Sbjct: 233 TSGIALSLPLGIALALGRQSNLPIIKGVCVVFIEFIRGVPLITLLFVASVMLAYFLPPGT 292

Query: 295 NFDLILRVVILVTLFAAAYIAEVIRGGLAALPRGQYEAADALGLDYWQAQRLIIMPQALK 354
           +FDL+LRV+I++TLFA+AYIAE IRGGLAALPRGQYEA D+LGLDYWQ+ RLII+PQALK
Sbjct: 293 SFDLVLRVIIMITLFASAYIAEAIRGGLAALPRGQYEAGDSLGLDYWQSMRLIILPQALK 352

Query: 355 ISIPGIVSSFIGLFKDTTLVAFVGLFDPLKGISNVVRSDMAWKGTYWEPYIFVALIFFLF 414
           ISIP IV+  IGLFKDTTLV+ + +FD L  I   + S   W G YWE   F  ++FF+F
Sbjct: 353 ISIPSIVNIAIGLFKDTTLVSIISMFDMLGMIQGPILSSTEWFGVYWELLGFAGVLFFVF 412

Query: 415 NFSMSRYSMYLERKLKRDHR 434
            + +S+YS +LER+L  +HR
Sbjct: 413 CYGISQYSQWLERQLATEHR 432


Lambda     K      H
   0.329    0.143    0.457 

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: 723
Number of extensions: 37
Number of successful extensions: 5
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: 434
Length of database: 432
Length adjustment: 32
Effective length of query: 402
Effective length of database: 400
Effective search space:   160800
Effective search space used:   160800
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 51 (24.3 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