GapMind for catabolism of small carbon sources

 

Alignments for a candidate for put1 in Aquimarina longa SW024

Align Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_062057831.1 N456_RS13080 proline dehydrogenase

Query= reanno::Pedo557:CA265_RS11605
         (394 letters)



>NCBI__GCF_001401755.1:WP_062057831.1
          Length = 390

 Score =  377 bits (969), Expect = e-109
 Identities = 183/384 (47%), Positives = 268/384 (69%)

Query: 11  FDNTEVAFRQKTNGELKKAYWLFKMIGSNFLTKVGPAITNFFLNIGLPIQGAIKATIFQQ 70
           FDNTE AF  K++ EL++AY+LFKMI +  L ++G A+TNF +   LP+QG I+AT+F  
Sbjct: 7   FDNTETAFVLKSDSELERAYFLFKMISNEPLVRIGTAVTNFAIKAHLPVQGLIRATVFDH 66

Query: 71  FCGGETIAECDKAIEQLHKGGVGTILDYSVEGEEEEQVFDETCAEIIRTIMRADGDVKIP 130
           FCGG +  +C   +++++   V ++LDYSVEG+EEE  FD    + I  +  AD    +P
Sbjct: 67  FCGGVSEQDCMPVVDKMYTKKVCSVLDYSVEGKEEEAQFDAVLKKTIDLLEFADEKDAMP 126

Query: 131 ITVFKITGIGRFALLQKLDAKETLNASEKAEYEKVKQRCEKICQTAFDKGVPIMIDAEET 190
             VFK TG+GRF + QK     +L   E+ E+ ++++R + +C+ A+D  V ++ID EE+
Sbjct: 127 FGVFKPTGLGRFLIWQKKTEGTSLTEEEEKEWNRIEERFDIVCKKAYDCDVALLIDGEES 186

Query: 191 WIQDTIDELALDMMRKFNRERIIVYNTYQMYRHDKLADMKADHLIAKADGFILGVKMVRG 250
           W+QD  DEL   MMRK+N+++ I+YNT Q+YRHD+LA ++  H  A+   F +GVK+VRG
Sbjct: 187 WMQDAADELVAKMMRKYNKDKAIIYNTLQLYRHDRLAYLQQLHEEARVYDFKIGVKIVRG 246

Query: 251 AYMEKERKRAAEMGYPSPIQPDKAASDRDYNESLRYCVDHIEEIAIVAGTHNEDSSRLLT 310
           AYMEKE +RA E GYP+PI  DK  +D++++ ++ Y   +I++I++  GTHNE+SS    
Sbjct: 247 AYMEKENERAKEKGYPTPICKDKQHTDQNFDMTMEYIFQNIKDISVFIGTHNEESSYKAM 306

Query: 311 YLLEEKNITHNHPHVYFAQLLGMSDNLSFNLADSNYNVAKYVPYGPIKAVMPYLFRRAQE 370
            L+++ +I  +   V+F QL GMSD++SFN A   YNVAKY+P+GP++ VMPYL RRA+E
Sbjct: 307 QLMKQFHIPKDDFRVWFGQLYGMSDHISFNQATKGYNVAKYLPFGPVRDVMPYLIRRAEE 366

Query: 371 NTSVAGQTGRELGLIERELKRRKL 394
           NTSVAGQT REL L+ +E KRRKL
Sbjct: 367 NTSVAGQTSRELNLLSQEKKRRKL 390


Lambda     K      H
   0.319    0.136    0.394 

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: 433
Number of extensions: 12
Number of successful extensions: 1
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: 394
Length of database: 390
Length adjustment: 31
Effective length of query: 363
Effective length of database: 359
Effective search space:   130317
Effective search space used:   130317
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)

This GapMind analysis is from Sep 24 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